Nickel in PDB 6qsu: Helicobacter Pylori Urease with Bme Bound in the Active Site
Enzymatic activity of Helicobacter Pylori Urease with Bme Bound in the Active Site
All present enzymatic activity of Helicobacter Pylori Urease with Bme Bound in the Active Site:
3.5.1.5;
Nickel Binding Sites:
Pages:
>>> Page 1 <<<
Page 2, Binding sites: 11 -
20;
Page 3, Binding sites: 21 -
24;
Binding sites:
The binding sites of Nickel atom in the Helicobacter Pylori Urease with Bme Bound in the Active Site
(pdb code 6qsu). This binding sites where shown within
5.0 Angstroms radius around Nickel atom.
In total 24 binding sites of Nickel where determined in the
Helicobacter Pylori Urease with Bme Bound in the Active Site, PDB code: 6qsu:
Jump to Nickel binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
9;
10;
Nickel binding site 1 out
of 24 in 6qsu
Go back to
Nickel Binding Sites List in 6qsu
Nickel binding site 1 out
of 24 in the Helicobacter Pylori Urease with Bme Bound in the Active Site
 Mono view
 Stereo pair view
|
|
A full contact list of Nickel with other atoms in the Ni binding
site number 1 of Helicobacter Pylori Urease with Bme Bound in the Active Site within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ni601
b:19.2
occ:1.00
|
NE2
|
B:HIS274
|
1.9
|
11.1
|
1.0
|
|
ND1
|
B:HIS248
|
2.0
|
10.5
|
1.0
|
|
S2
|
B:BME603
|
2.1
|
12.8
|
1.0
|
|
OQ2
|
B:KCX219
|
2.2
|
6.1
|
1.0
|
|
CE1
|
B:HIS248
|
2.8
|
10.5
|
1.0
|
|
CE1
|
B:HIS274
|
2.8
|
11.1
|
1.0
|
|
CD2
|
B:HIS274
|
3.0
|
11.1
|
1.0
|
|
CG
|
B:HIS248
|
3.1
|
10.5
|
1.0
|
|
CX
|
B:KCX219
|
3.2
|
6.1
|
1.0
|
|
NI
|
B:NI602
|
3.3
|
14.1
|
1.0
|
|
OQ1
|
B:KCX219
|
3.4
|
6.1
|
1.0
|
|
CB
|
B:HIS248
|
3.6
|
10.5
|
1.0
|
|
O1
|
B:BME603
|
3.7
|
12.8
|
1.0
|
|
O
|
B:GLY279
|
3.7
|
15.0
|
1.0
|
|
C2
|
B:BME603
|
3.7
|
12.8
|
1.0
|
|
NE2
|
B:HIS221
|
3.7
|
9.4
|
1.0
|
|
ND1
|
B:HIS274
|
4.0
|
11.1
|
1.0
|
|
NE2
|
B:HIS248
|
4.0
|
10.5
|
1.0
|
|
CE1
|
B:HIS136
|
4.0
|
7.8
|
1.0
|
|
CG
|
B:HIS274
|
4.1
|
11.1
|
1.0
|
|
NE2
|
B:HIS136
|
4.1
|
7.8
|
1.0
|
|
CD2
|
B:HIS221
|
4.1
|
9.4
|
1.0
|
|
C1
|
B:BME603
|
4.1
|
12.8
|
1.0
|
|
CD2
|
B:HIS248
|
4.1
|
10.5
|
1.0
|
|
OD2
|
B:ASP362
|
4.3
|
10.2
|
1.0
|
|
NZ
|
B:KCX219
|
4.4
|
6.1
|
1.0
|
|
OD1
|
B:ASP362
|
4.7
|
10.2
|
1.0
|
|
CE1
|
B:HIS221
|
4.7
|
9.4
|
1.0
|
|
C
|
B:GLY279
|
4.7
|
15.0
|
1.0
|
|
CA
|
B:HIS248
|
4.7
|
10.5
|
1.0
|
|
CB
|
B:PHE273
|
4.7
|
8.3
|
1.0
|
|
CE
|
B:KCX219
|
4.9
|
6.1
|
1.0
|
|
CG
|
B:ASP362
|
4.9
|
10.2
|
1.0
|
|
Nickel binding site 2 out
of 24 in 6qsu
Go back to
Nickel Binding Sites List in 6qsu
Nickel binding site 2 out
of 24 in the Helicobacter Pylori Urease with Bme Bound in the Active Site
 Mono view
 Stereo pair view
|
|
A full contact list of Nickel with other atoms in the Ni binding
site number 2 of Helicobacter Pylori Urease with Bme Bound in the Active Site within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ni602
b:14.1
occ:1.00
|
OD1
|
B:ASP362
|
2.0
|
10.2
|
1.0
|
|
OQ1
|
B:KCX219
|
2.1
|
6.1
|
1.0
|
|
NE2
|
B:HIS136
|
2.1
|
7.8
|
1.0
|
|
NE2
|
B:HIS138
|
2.2
|
6.1
|
1.0
|
|
S2
|
B:BME603
|
2.6
|
12.8
|
1.0
|
|
CG
|
B:ASP362
|
2.9
|
10.2
|
1.0
|
|
CE1
|
B:HIS136
|
3.0
|
7.8
|
1.0
|
|
CX
|
B:KCX219
|
3.0
|
6.1
|
1.0
|
|
CE1
|
B:HIS138
|
3.0
|
6.1
|
1.0
|
|
CD2
|
B:HIS136
|
3.1
|
7.8
|
1.0
|
|
C2
|
B:BME603
|
3.2
|
12.8
|
1.0
|
|
CD2
|
B:HIS138
|
3.3
|
6.1
|
1.0
|
|
OQ2
|
B:KCX219
|
3.3
|
6.1
|
1.0
|
|
OD2
|
B:ASP362
|
3.3
|
10.2
|
1.0
|
|
NI
|
B:NI601
|
3.3
|
19.2
|
1.0
|
|
CG2
|
B:THR171
|
3.9
|
4.8
|
1.0
|
|
ND1
|
B:HIS136
|
4.1
|
7.8
|
1.0
|
|
NZ
|
B:KCX219
|
4.1
|
6.1
|
1.0
|
|
CB
|
B:ASP362
|
4.2
|
10.2
|
1.0
|
|
CG
|
B:HIS136
|
4.2
|
7.8
|
1.0
|
|
ND1
|
B:HIS138
|
4.2
|
6.1
|
1.0
|
|
CG
|
B:HIS138
|
4.3
|
6.1
|
1.0
|
|
O1
|
B:BME603
|
4.4
|
12.8
|
1.0
|
|
C1
|
B:BME603
|
4.4
|
12.8
|
1.0
|
|
NE2
|
B:HIS274
|
4.4
|
11.1
|
1.0
|
|
O
|
B:ALA169
|
4.5
|
8.4
|
1.0
|
|
CA
|
B:ASP362
|
4.5
|
10.2
|
1.0
|
|
CD2
|
B:HIS274
|
4.6
|
11.1
|
1.0
|
|
CB
|
B:ALA365
|
4.6
|
12.9
|
1.0
|
|
O
|
B:ALA365
|
4.8
|
12.9
|
1.0
|
|
NE2
|
B:HIS221
|
4.9
|
9.4
|
1.0
|
|
CD2
|
B:PHE273
|
4.9
|
8.3
|
1.0
|
|
Nickel binding site 3 out
of 24 in 6qsu
Go back to
Nickel Binding Sites List in 6qsu
Nickel binding site 3 out
of 24 in the Helicobacter Pylori Urease with Bme Bound in the Active Site
 Mono view
 Stereo pair view
|
|
A full contact list of Nickel with other atoms in the Ni binding
site number 3 of Helicobacter Pylori Urease with Bme Bound in the Active Site within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
J:Ni601
b:19.5
occ:1.00
|
NE2
|
J:HIS274
|
1.9
|
11.1
|
1.0
|
|
ND1
|
J:HIS248
|
2.0
|
10.3
|
1.0
|
|
S2
|
J:BME603
|
2.2
|
13.1
|
1.0
|
|
OQ2
|
J:KCX219
|
2.2
|
6.0
|
1.0
|
|
CE1
|
J:HIS248
|
2.8
|
10.3
|
1.0
|
|
CE1
|
J:HIS274
|
2.8
|
11.1
|
1.0
|
|
CD2
|
J:HIS274
|
3.0
|
11.1
|
1.0
|
|
CG
|
J:HIS248
|
3.1
|
10.3
|
1.0
|
|
CX
|
J:KCX219
|
3.2
|
6.0
|
1.0
|
|
NI
|
J:NI602
|
3.3
|
15.0
|
1.0
|
|
OQ1
|
J:KCX219
|
3.4
|
6.0
|
1.0
|
|
CB
|
J:HIS248
|
3.6
|
10.3
|
1.0
|
|
O1
|
J:BME603
|
3.7
|
13.1
|
1.0
|
|
O
|
J:GLY279
|
3.7
|
14.8
|
1.0
|
|
C2
|
J:BME603
|
3.7
|
13.1
|
1.0
|
|
NE2
|
J:HIS221
|
3.7
|
8.7
|
1.0
|
|
ND1
|
J:HIS274
|
4.0
|
11.1
|
1.0
|
|
NE2
|
J:HIS248
|
4.0
|
10.3
|
1.0
|
|
CE1
|
J:HIS136
|
4.0
|
7.4
|
1.0
|
|
CG
|
J:HIS274
|
4.1
|
11.1
|
1.0
|
|
NE2
|
J:HIS136
|
4.1
|
7.4
|
1.0
|
|
CD2
|
J:HIS221
|
4.1
|
8.7
|
1.0
|
|
C1
|
J:BME603
|
4.1
|
13.1
|
1.0
|
|
CD2
|
J:HIS248
|
4.1
|
10.3
|
1.0
|
|
OD2
|
J:ASP362
|
4.3
|
10.2
|
1.0
|
|
NZ
|
J:KCX219
|
4.4
|
6.0
|
1.0
|
|
OD1
|
J:ASP362
|
4.7
|
10.2
|
1.0
|
|
CE1
|
J:HIS221
|
4.7
|
8.7
|
1.0
|
|
C
|
J:GLY279
|
4.7
|
14.8
|
1.0
|
|
CA
|
J:HIS248
|
4.7
|
10.3
|
1.0
|
|
CB
|
J:PHE273
|
4.7
|
8.1
|
1.0
|
|
CE
|
J:KCX219
|
4.9
|
6.0
|
1.0
|
|
CG
|
J:ASP362
|
4.9
|
10.2
|
1.0
|
|
Nickel binding site 4 out
of 24 in 6qsu
Go back to
Nickel Binding Sites List in 6qsu
Nickel binding site 4 out
of 24 in the Helicobacter Pylori Urease with Bme Bound in the Active Site
 Mono view
 Stereo pair view
|
|
A full contact list of Nickel with other atoms in the Ni binding
site number 4 of Helicobacter Pylori Urease with Bme Bound in the Active Site within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
J:Ni602
b:15.0
occ:1.00
|
OD1
|
J:ASP362
|
2.0
|
10.2
|
1.0
|
|
OQ1
|
J:KCX219
|
2.1
|
6.0
|
1.0
|
|
NE2
|
J:HIS136
|
2.1
|
7.4
|
1.0
|
|
NE2
|
J:HIS138
|
2.2
|
5.9
|
1.0
|
|
S2
|
J:BME603
|
2.6
|
13.1
|
1.0
|
|
CG
|
J:ASP362
|
2.9
|
10.2
|
1.0
|
|
CE1
|
J:HIS136
|
3.0
|
7.4
|
1.0
|
|
CX
|
J:KCX219
|
3.0
|
6.0
|
1.0
|
|
CE1
|
J:HIS138
|
3.0
|
5.9
|
1.0
|
|
CD2
|
J:HIS136
|
3.1
|
7.4
|
1.0
|
|
C2
|
J:BME603
|
3.2
|
13.1
|
1.0
|
|
CD2
|
J:HIS138
|
3.3
|
5.9
|
1.0
|
|
OQ2
|
J:KCX219
|
3.3
|
6.0
|
1.0
|
|
OD2
|
J:ASP362
|
3.3
|
10.2
|
1.0
|
|
NI
|
J:NI601
|
3.3
|
19.5
|
1.0
|
|
CG2
|
J:THR171
|
3.9
|
4.5
|
1.0
|
|
ND1
|
J:HIS136
|
4.1
|
7.4
|
1.0
|
|
NZ
|
J:KCX219
|
4.1
|
6.0
|
1.0
|
|
CB
|
J:ASP362
|
4.2
|
10.2
|
1.0
|
|
CG
|
J:HIS136
|
4.2
|
7.4
|
1.0
|
|
ND1
|
J:HIS138
|
4.2
|
5.9
|
1.0
|
|
CG
|
J:HIS138
|
4.3
|
5.9
|
1.0
|
|
O1
|
J:BME603
|
4.4
|
13.1
|
1.0
|
|
C1
|
J:BME603
|
4.4
|
13.1
|
1.0
|
|
NE2
|
J:HIS274
|
4.4
|
11.1
|
1.0
|
|
O
|
J:ALA169
|
4.5
|
8.4
|
1.0
|
|
CA
|
J:ASP362
|
4.5
|
10.2
|
1.0
|
|
CD2
|
J:HIS274
|
4.6
|
11.1
|
1.0
|
|
CB
|
J:ALA365
|
4.6
|
12.9
|
1.0
|
|
O
|
J:ALA365
|
4.8
|
12.9
|
1.0
|
|
NE2
|
J:HIS221
|
4.9
|
8.7
|
1.0
|
|
CD2
|
J:PHE273
|
4.9
|
8.1
|
1.0
|
|
Nickel binding site 5 out
of 24 in 6qsu
Go back to
Nickel Binding Sites List in 6qsu
Nickel binding site 5 out
of 24 in the Helicobacter Pylori Urease with Bme Bound in the Active Site
 Mono view
 Stereo pair view
|
|
A full contact list of Nickel with other atoms in the Ni binding
site number 5 of Helicobacter Pylori Urease with Bme Bound in the Active Site within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Ni601
b:17.1
occ:1.00
|
NE2
|
D:HIS274
|
1.9
|
10.3
|
1.0
|
|
ND1
|
D:HIS248
|
2.0
|
9.7
|
1.0
|
|
S2
|
D:BME603
|
2.1
|
12.2
|
1.0
|
|
OQ2
|
D:KCX219
|
2.2
|
5.5
|
1.0
|
|
CE1
|
D:HIS248
|
2.8
|
9.7
|
1.0
|
|
CE1
|
D:HIS274
|
2.8
|
10.3
|
1.0
|
|
CD2
|
D:HIS274
|
3.0
|
10.3
|
1.0
|
|
CG
|
D:HIS248
|
3.1
|
9.7
|
1.0
|
|
CX
|
D:KCX219
|
3.2
|
5.5
|
1.0
|
|
NI
|
D:NI602
|
3.3
|
12.4
|
1.0
|
|
OQ1
|
D:KCX219
|
3.4
|
5.5
|
1.0
|
|
CB
|
D:HIS248
|
3.6
|
9.7
|
1.0
|
|
O1
|
D:BME603
|
3.7
|
12.2
|
1.0
|
|
O
|
D:GLY279
|
3.7
|
14.2
|
1.0
|
|
C2
|
D:BME603
|
3.7
|
12.2
|
1.0
|
|
NE2
|
D:HIS221
|
3.7
|
8.7
|
1.0
|
|
ND1
|
D:HIS274
|
4.0
|
10.3
|
1.0
|
|
NE2
|
D:HIS248
|
4.0
|
9.7
|
1.0
|
|
CE1
|
D:HIS136
|
4.0
|
6.9
|
1.0
|
|
CG
|
D:HIS274
|
4.1
|
10.3
|
1.0
|
|
NE2
|
D:HIS136
|
4.1
|
6.9
|
1.0
|
|
CD2
|
D:HIS221
|
4.1
|
8.7
|
1.0
|
|
C1
|
D:BME603
|
4.1
|
12.2
|
1.0
|
|
CD2
|
D:HIS248
|
4.1
|
9.7
|
1.0
|
|
OD2
|
D:ASP362
|
4.3
|
9.5
|
1.0
|
|
NZ
|
D:KCX219
|
4.4
|
5.5
|
1.0
|
|
OD1
|
D:ASP362
|
4.7
|
9.5
|
1.0
|
|
CE1
|
D:HIS221
|
4.7
|
8.7
|
1.0
|
|
C
|
D:GLY279
|
4.7
|
14.2
|
1.0
|
|
CA
|
D:HIS248
|
4.7
|
9.7
|
1.0
|
|
CB
|
D:PHE273
|
4.7
|
7.8
|
1.0
|
|
CE
|
D:KCX219
|
4.9
|
5.5
|
1.0
|
|
CG
|
D:ASP362
|
4.9
|
9.5
|
1.0
|
|
Nickel binding site 6 out
of 24 in 6qsu
Go back to
Nickel Binding Sites List in 6qsu
Nickel binding site 6 out
of 24 in the Helicobacter Pylori Urease with Bme Bound in the Active Site
 Mono view
 Stereo pair view
|
|
A full contact list of Nickel with other atoms in the Ni binding
site number 6 of Helicobacter Pylori Urease with Bme Bound in the Active Site within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Ni602
b:12.4
occ:1.00
|
OD1
|
D:ASP362
|
2.0
|
9.5
|
1.0
|
|
OQ1
|
D:KCX219
|
2.1
|
5.5
|
1.0
|
|
NE2
|
D:HIS136
|
2.1
|
6.9
|
1.0
|
|
NE2
|
D:HIS138
|
2.2
|
5.3
|
1.0
|
|
S2
|
D:BME603
|
2.6
|
12.2
|
1.0
|
|
CG
|
D:ASP362
|
2.9
|
9.5
|
1.0
|
|
CE1
|
D:HIS136
|
3.0
|
6.9
|
1.0
|
|
CX
|
D:KCX219
|
3.0
|
5.5
|
1.0
|
|
CE1
|
D:HIS138
|
3.0
|
5.3
|
1.0
|
|
CD2
|
D:HIS136
|
3.1
|
6.9
|
1.0
|
|
C2
|
D:BME603
|
3.2
|
12.2
|
1.0
|
|
CD2
|
D:HIS138
|
3.3
|
5.3
|
1.0
|
|
OQ2
|
D:KCX219
|
3.3
|
5.5
|
1.0
|
|
OD2
|
D:ASP362
|
3.3
|
9.5
|
1.0
|
|
NI
|
D:NI601
|
3.3
|
17.1
|
1.0
|
|
CG2
|
D:THR171
|
3.9
|
4.3
|
1.0
|
|
ND1
|
D:HIS136
|
4.1
|
6.9
|
1.0
|
|
NZ
|
D:KCX219
|
4.1
|
5.5
|
1.0
|
|
CB
|
D:ASP362
|
4.2
|
9.5
|
1.0
|
|
CG
|
D:HIS136
|
4.2
|
6.9
|
1.0
|
|
ND1
|
D:HIS138
|
4.2
|
5.3
|
1.0
|
|
CG
|
D:HIS138
|
4.3
|
5.3
|
1.0
|
|
O1
|
D:BME603
|
4.4
|
12.2
|
1.0
|
|
C1
|
D:BME603
|
4.4
|
12.2
|
1.0
|
|
NE2
|
D:HIS274
|
4.4
|
10.3
|
1.0
|
|
O
|
D:ALA169
|
4.5
|
7.5
|
1.0
|
|
CA
|
D:ASP362
|
4.5
|
9.5
|
1.0
|
|
CD2
|
D:HIS274
|
4.6
|
10.3
|
1.0
|
|
CB
|
D:ALA365
|
4.6
|
11.8
|
1.0
|
|
O
|
D:ALA365
|
4.8
|
11.8
|
1.0
|
|
NE2
|
D:HIS221
|
4.9
|
8.7
|
1.0
|
|
CD2
|
D:PHE273
|
4.9
|
7.8
|
1.0
|
|
Nickel binding site 7 out
of 24 in 6qsu
Go back to
Nickel Binding Sites List in 6qsu
Nickel binding site 7 out
of 24 in the Helicobacter Pylori Urease with Bme Bound in the Active Site
 Mono view
 Stereo pair view
|
|
A full contact list of Nickel with other atoms in the Ni binding
site number 7 of Helicobacter Pylori Urease with Bme Bound in the Active Site within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:Ni601
b:20.0
occ:1.00
|
NE2
|
F:HIS274
|
1.9
|
11.2
|
1.0
|
|
ND1
|
F:HIS248
|
2.0
|
9.9
|
1.0
|
|
S2
|
F:BME603
|
2.1
|
13.0
|
1.0
|
|
OQ1
|
F:KCX219
|
2.2
|
5.9
|
1.0
|
|
CE1
|
F:HIS248
|
2.8
|
9.9
|
1.0
|
|
CE1
|
F:HIS274
|
2.8
|
11.2
|
1.0
|
|
CD2
|
F:HIS274
|
3.0
|
11.2
|
1.0
|
|
CG
|
F:HIS248
|
3.1
|
9.9
|
1.0
|
|
CX
|
F:KCX219
|
3.2
|
5.9
|
1.0
|
|
NI
|
F:NI602
|
3.3
|
14.8
|
1.0
|
|
OQ2
|
F:KCX219
|
3.4
|
5.9
|
1.0
|
|
CB
|
F:HIS248
|
3.6
|
9.9
|
1.0
|
|
O1
|
F:BME603
|
3.7
|
13.0
|
1.0
|
|
O
|
F:GLY279
|
3.7
|
15.9
|
1.0
|
|
C2
|
F:BME603
|
3.7
|
13.0
|
1.0
|
|
NE2
|
F:HIS221
|
3.7
|
8.5
|
1.0
|
|
ND1
|
F:HIS274
|
4.0
|
11.2
|
1.0
|
|
NE2
|
F:HIS248
|
4.0
|
9.9
|
1.0
|
|
CE1
|
F:HIS136
|
4.0
|
7.8
|
1.0
|
|
CG
|
F:HIS274
|
4.1
|
11.2
|
1.0
|
|
NE2
|
F:HIS136
|
4.1
|
7.8
|
1.0
|
|
CD2
|
F:HIS221
|
4.1
|
8.5
|
1.0
|
|
C1
|
F:BME603
|
4.1
|
13.0
|
1.0
|
|
CD2
|
F:HIS248
|
4.1
|
9.9
|
1.0
|
|
OD2
|
F:ASP362
|
4.3
|
10.3
|
1.0
|
|
NZ
|
F:KCX219
|
4.4
|
5.9
|
1.0
|
|
OD1
|
F:ASP362
|
4.7
|
10.3
|
1.0
|
|
CE1
|
F:HIS221
|
4.7
|
8.5
|
1.0
|
|
C
|
F:GLY279
|
4.7
|
15.9
|
1.0
|
|
CA
|
F:HIS248
|
4.7
|
9.9
|
1.0
|
|
CB
|
F:PHE273
|
4.7
|
8.5
|
1.0
|
|
CE
|
F:KCX219
|
4.9
|
5.9
|
1.0
|
|
CG
|
F:ASP362
|
4.9
|
10.3
|
1.0
|
|
Nickel binding site 8 out
of 24 in 6qsu
Go back to
Nickel Binding Sites List in 6qsu
Nickel binding site 8 out
of 24 in the Helicobacter Pylori Urease with Bme Bound in the Active Site
 Mono view
 Stereo pair view
|
|
A full contact list of Nickel with other atoms in the Ni binding
site number 8 of Helicobacter Pylori Urease with Bme Bound in the Active Site within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:Ni602
b:14.8
occ:1.00
|
OD1
|
F:ASP362
|
2.0
|
10.3
|
1.0
|
|
OQ2
|
F:KCX219
|
2.1
|
5.9
|
1.0
|
|
NE2
|
F:HIS136
|
2.1
|
7.8
|
1.0
|
|
NE2
|
F:HIS138
|
2.2
|
5.9
|
1.0
|
|
S2
|
F:BME603
|
2.6
|
13.0
|
1.0
|
|
CG
|
F:ASP362
|
2.9
|
10.3
|
1.0
|
|
CE1
|
F:HIS136
|
3.0
|
7.8
|
1.0
|
|
CX
|
F:KCX219
|
3.0
|
5.9
|
1.0
|
|
CE1
|
F:HIS138
|
3.0
|
5.9
|
1.0
|
|
CD2
|
F:HIS136
|
3.1
|
7.8
|
1.0
|
|
C2
|
F:BME603
|
3.2
|
13.0
|
1.0
|
|
CD2
|
F:HIS138
|
3.3
|
5.9
|
1.0
|
|
OQ1
|
F:KCX219
|
3.3
|
5.9
|
1.0
|
|
OD2
|
F:ASP362
|
3.3
|
10.3
|
1.0
|
|
NI
|
F:NI601
|
3.3
|
20.0
|
1.0
|
|
CG2
|
F:THR171
|
3.9
|
5.0
|
1.0
|
|
ND1
|
F:HIS136
|
4.1
|
7.8
|
1.0
|
|
NZ
|
F:KCX219
|
4.1
|
5.9
|
1.0
|
|
CB
|
F:ASP362
|
4.2
|
10.3
|
1.0
|
|
CG
|
F:HIS136
|
4.2
|
7.8
|
1.0
|
|
ND1
|
F:HIS138
|
4.2
|
5.9
|
1.0
|
|
CG
|
F:HIS138
|
4.3
|
5.9
|
1.0
|
|
O1
|
F:BME603
|
4.4
|
13.0
|
1.0
|
|
C1
|
F:BME603
|
4.4
|
13.0
|
1.0
|
|
NE2
|
F:HIS274
|
4.4
|
11.2
|
1.0
|
|
O
|
F:ALA169
|
4.5
|
8.0
|
1.0
|
|
CA
|
F:ASP362
|
4.5
|
10.3
|
1.0
|
|
CD2
|
F:HIS274
|
4.6
|
11.2
|
1.0
|
|
CB
|
F:ALA365
|
4.6
|
12.6
|
1.0
|
|
O
|
F:ALA365
|
4.8
|
12.6
|
1.0
|
|
NE2
|
F:HIS221
|
4.9
|
8.5
|
1.0
|
|
CD2
|
F:PHE273
|
4.9
|
8.5
|
1.0
|
|
Nickel binding site 9 out
of 24 in 6qsu
Go back to
Nickel Binding Sites List in 6qsu
Nickel binding site 9 out
of 24 in the Helicobacter Pylori Urease with Bme Bound in the Active Site
 Mono view
 Stereo pair view
|
|
A full contact list of Nickel with other atoms in the Ni binding
site number 9 of Helicobacter Pylori Urease with Bme Bound in the Active Site within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
H:Ni601
b:18.2
occ:1.00
|
NE2
|
H:HIS274
|
1.9
|
10.6
|
1.0
|
|
ND1
|
H:HIS248
|
2.0
|
9.6
|
1.0
|
|
S2
|
H:BME603
|
2.1
|
11.4
|
1.0
|
|
OQ1
|
H:KCX219
|
2.2
|
5.8
|
1.0
|
|
CE1
|
H:HIS248
|
2.8
|
9.6
|
1.0
|
|
CE1
|
H:HIS274
|
2.8
|
10.6
|
1.0
|
|
CD2
|
H:HIS274
|
3.0
|
10.6
|
1.0
|
|
CG
|
H:HIS248
|
3.1
|
9.6
|
1.0
|
|
CX
|
H:KCX219
|
3.2
|
5.8
|
1.0
|
|
NI
|
H:NI602
|
3.3
|
11.9
|
1.0
|
|
OQ2
|
H:KCX219
|
3.4
|
5.8
|
1.0
|
|
CB
|
H:HIS248
|
3.6
|
9.6
|
1.0
|
|
O1
|
H:BME603
|
3.7
|
11.4
|
1.0
|
|
O
|
H:GLY279
|
3.7
|
15.2
|
1.0
|
|
C2
|
H:BME603
|
3.7
|
11.4
|
1.0
|
|
NE2
|
H:HIS221
|
3.7
|
8.4
|
1.0
|
|
ND1
|
H:HIS274
|
4.0
|
10.6
|
1.0
|
|
NE2
|
H:HIS248
|
4.0
|
9.6
|
1.0
|
|
CE1
|
H:HIS136
|
4.0
|
7.3
|
1.0
|
|
CG
|
H:HIS274
|
4.1
|
10.6
|
1.0
|
|
NE2
|
H:HIS136
|
4.1
|
7.3
|
1.0
|
|
CD2
|
H:HIS221
|
4.1
|
8.4
|
1.0
|
|
C1
|
H:BME603
|
4.1
|
11.4
|
1.0
|
|
CD2
|
H:HIS248
|
4.1
|
9.6
|
1.0
|
|
OD2
|
H:ASP362
|
4.3
|
10.2
|
1.0
|
|
NZ
|
H:KCX219
|
4.4
|
5.8
|
1.0
|
|
OD1
|
H:ASP362
|
4.7
|
10.2
|
1.0
|
|
CE1
|
H:HIS221
|
4.7
|
8.4
|
1.0
|
|
C
|
H:GLY279
|
4.7
|
15.2
|
1.0
|
|
CA
|
H:HIS248
|
4.7
|
9.6
|
1.0
|
|
CB
|
H:PHE273
|
4.7
|
7.7
|
1.0
|
|
CE
|
H:KCX219
|
4.9
|
5.8
|
1.0
|
|
CG
|
H:ASP362
|
4.9
|
10.2
|
1.0
|
|
Nickel binding site 10 out
of 24 in 6qsu
Go back to
Nickel Binding Sites List in 6qsu
Nickel binding site 10 out
of 24 in the Helicobacter Pylori Urease with Bme Bound in the Active Site
 Mono view
 Stereo pair view
|
|
A full contact list of Nickel with other atoms in the Ni binding
site number 10 of Helicobacter Pylori Urease with Bme Bound in the Active Site within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
H:Ni602
b:11.9
occ:1.00
|
OD1
|
H:ASP362
|
2.0
|
10.2
|
1.0
|
|
OQ2
|
H:KCX219
|
2.1
|
5.8
|
1.0
|
|
NE2
|
H:HIS136
|
2.1
|
7.3
|
1.0
|
|
NE2
|
H:HIS138
|
2.2
|
5.7
|
1.0
|
|
S2
|
H:BME603
|
2.6
|
11.4
|
1.0
|
|
CG
|
H:ASP362
|
2.9
|
10.2
|
1.0
|
|
CE1
|
H:HIS136
|
3.0
|
7.3
|
1.0
|
|
CX
|
H:KCX219
|
3.0
|
5.8
|
1.0
|
|
CE1
|
H:HIS138
|
3.0
|
5.7
|
1.0
|
|
CD2
|
H:HIS136
|
3.1
|
7.3
|
1.0
|
|
C2
|
H:BME603
|
3.2
|
11.4
|
1.0
|
|
CD2
|
H:HIS138
|
3.3
|
5.7
|
1.0
|
|
OQ1
|
H:KCX219
|
3.3
|
5.8
|
1.0
|
|
OD2
|
H:ASP362
|
3.3
|
10.2
|
1.0
|
|
NI
|
H:NI601
|
3.3
|
18.2
|
1.0
|
|
CG2
|
H:THR171
|
3.9
|
4.5
|
1.0
|
|
ND1
|
H:HIS136
|
4.1
|
7.3
|
1.0
|
|
NZ
|
H:KCX219
|
4.1
|
5.8
|
1.0
|
|
CB
|
H:ASP362
|
4.2
|
10.2
|
1.0
|
|
CG
|
H:HIS136
|
4.2
|
7.3
|
1.0
|
|
ND1
|
H:HIS138
|
4.2
|
5.7
|
1.0
|
|
CG
|
H:HIS138
|
4.3
|
5.7
|
1.0
|
|
O1
|
H:BME603
|
4.4
|
11.4
|
1.0
|
|
C1
|
H:BME603
|
4.4
|
11.4
|
1.0
|
|
NE2
|
H:HIS274
|
4.4
|
10.6
|
1.0
|
|
O
|
H:ALA169
|
4.5
|
7.0
|
1.0
|
|
CA
|
H:ASP362
|
4.5
|
10.2
|
1.0
|
|
CD2
|
H:HIS274
|
4.6
|
10.6
|
1.0
|
|
CB
|
H:ALA365
|
4.6
|
13.1
|
1.0
|
|
O
|
H:ALA365
|
4.8
|
13.1
|
1.0
|
|
NE2
|
H:HIS221
|
4.9
|
8.4
|
1.0
|
|
CD2
|
H:PHE273
|
4.9
|
7.7
|
1.0
|
|
Reference:
H.Luecke,
E.Cunha.
Helicobacter Pylori Urease with Bme in the Active Site To Be Published.
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