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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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.
Page generated: Mon Jan 25 15:58:05 2021

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