Nickel in PDB 4mgg: Crystal Structure of An Enolase (Mandelate Racemase Subgroup) From Labrenzia Aggregata Iam 12614 (Target Nysgrc-012903) with Bound Mg, Space Group P212121
Protein crystallography data
The structure of Crystal Structure of An Enolase (Mandelate Racemase Subgroup) From Labrenzia Aggregata Iam 12614 (Target Nysgrc-012903) with Bound Mg, Space Group P212121, PDB code: 4mgg
was solved by
M.W.Vetting,
X.Zhang,
S.R.Wasserman,
L.L.Morisco,
S.Sojitra,
J.B.Bonanno,
J.A.Gerlt,
S.C.Almo,
New York Structural Genomics Research Consortium(Nysgrc),
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
40.81 /
2.20
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
110.313,
154.897,
181.983,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
15 /
21.6
|
Other elements in 4mgg:
The structure of Crystal Structure of An Enolase (Mandelate Racemase Subgroup) From Labrenzia Aggregata Iam 12614 (Target Nysgrc-012903) with Bound Mg, Space Group P212121 also contains other interesting chemical elements:
Nickel Binding Sites:
The binding sites of Nickel atom in the Crystal Structure of An Enolase (Mandelate Racemase Subgroup) From Labrenzia Aggregata Iam 12614 (Target Nysgrc-012903) with Bound Mg, Space Group P212121
(pdb code 4mgg). This binding sites where shown within
5.0 Angstroms radius around Nickel atom.
In total 3 binding sites of Nickel where determined in the
Crystal Structure of An Enolase (Mandelate Racemase Subgroup) From Labrenzia Aggregata Iam 12614 (Target Nysgrc-012903) with Bound Mg, Space Group P212121, PDB code: 4mgg:
Jump to Nickel binding site number:
1;
2;
3;
Nickel binding site 1 out
of 3 in 4mgg
Go back to
Nickel Binding Sites List in 4mgg
Nickel binding site 1 out
of 3 in the Crystal Structure of An Enolase (Mandelate Racemase Subgroup) From Labrenzia Aggregata Iam 12614 (Target Nysgrc-012903) with Bound Mg, Space Group P212121
 Mono view
 Stereo pair view
|
A full contact list of Nickel with other atoms in the Ni binding
site number 1 of Crystal Structure of An Enolase (Mandelate Racemase Subgroup) From Labrenzia Aggregata Iam 12614 (Target Nysgrc-012903) with Bound Mg, Space Group P212121 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ni402
b:18.1
occ:1.00
|
O
|
G:HOH502
|
2.0
|
19.7
|
1.0
|
O
|
A:HOH501
|
2.0
|
9.8
|
1.0
|
O
|
A:HOH502
|
2.0
|
13.5
|
1.0
|
NE2
|
G:HIS98
|
2.0
|
16.6
|
1.0
|
NE2
|
A:HIS98
|
2.2
|
14.8
|
1.0
|
O
|
G:HOH501
|
2.2
|
11.3
|
1.0
|
CE1
|
G:HIS98
|
3.0
|
16.4
|
1.0
|
CD2
|
G:HIS98
|
3.0
|
16.9
|
1.0
|
CE1
|
A:HIS98
|
3.1
|
17.6
|
1.0
|
CD2
|
A:HIS98
|
3.2
|
14.0
|
1.0
|
HE1
|
G:HIS98
|
3.2
|
19.7
|
1.0
|
HD2
|
G:HIS98
|
3.2
|
20.2
|
1.0
|
HE1
|
A:HIS98
|
3.3
|
21.1
|
1.0
|
HD2
|
A:HIS98
|
3.3
|
16.8
|
1.0
|
HG
|
G:SER67
|
3.7
|
27.1
|
1.0
|
HG
|
A:SER67
|
3.8
|
29.1
|
1.0
|
OG
|
G:SER67
|
4.0
|
22.6
|
1.0
|
OG
|
A:SER67
|
4.1
|
24.3
|
1.0
|
OE2
|
G:GLU71
|
4.1
|
31.5
|
1.0
|
ND1
|
G:HIS98
|
4.1
|
16.0
|
1.0
|
CG
|
G:HIS98
|
4.2
|
15.8
|
1.0
|
OE2
|
A:GLU71
|
4.2
|
33.6
|
1.0
|
ND1
|
A:HIS98
|
4.2
|
14.4
|
1.0
|
HD11
|
G:LEU95
|
4.3
|
20.3
|
1.0
|
CG
|
A:HIS98
|
4.3
|
14.0
|
1.0
|
OE1
|
G:GLU71
|
4.4
|
36.5
|
1.0
|
OE1
|
A:GLU71
|
4.4
|
31.2
|
1.0
|
O
|
G:HOH533
|
4.5
|
21.0
|
1.0
|
O
|
G:HOH521
|
4.5
|
13.9
|
1.0
|
HD11
|
A:LEU95
|
4.5
|
26.3
|
1.0
|
HA2
|
A:GLY64
|
4.6
|
17.3
|
1.0
|
CD
|
G:GLU71
|
4.7
|
24.9
|
1.0
|
HA2
|
G:GLY68
|
4.7
|
20.3
|
1.0
|
CD
|
A:GLU71
|
4.7
|
30.6
|
1.0
|
HA2
|
A:GLY68
|
4.7
|
17.2
|
1.0
|
HA2
|
G:GLY64
|
4.8
|
26.6
|
1.0
|
HD1
|
G:HIS98
|
4.9
|
19.2
|
1.0
|
|
Nickel binding site 2 out
of 3 in 4mgg
Go back to
Nickel Binding Sites List in 4mgg
Nickel binding site 2 out
of 3 in the Crystal Structure of An Enolase (Mandelate Racemase Subgroup) From Labrenzia Aggregata Iam 12614 (Target Nysgrc-012903) with Bound Mg, Space Group P212121
 Mono view
 Stereo pair view
|
A full contact list of Nickel with other atoms in the Ni binding
site number 2 of Crystal Structure of An Enolase (Mandelate Racemase Subgroup) From Labrenzia Aggregata Iam 12614 (Target Nysgrc-012903) with Bound Mg, Space Group P212121 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Ni401
b:29.0
occ:1.00
|
O
|
E:HOH803
|
2.1
|
20.7
|
1.0
|
NE2
|
E:HIS98
|
2.1
|
32.3
|
1.0
|
O
|
E:HOH802
|
2.1
|
22.4
|
1.0
|
O
|
C:HOH502
|
2.2
|
27.0
|
1.0
|
O
|
C:HOH501
|
2.2
|
27.7
|
1.0
|
NE2
|
C:HIS98
|
2.2
|
28.5
|
1.0
|
CE1
|
E:HIS98
|
3.0
|
29.8
|
1.0
|
CE1
|
C:HIS98
|
3.1
|
29.8
|
1.0
|
HE1
|
C:HIS98
|
3.2
|
35.7
|
1.0
|
HE1
|
E:HIS98
|
3.2
|
35.8
|
1.0
|
CD2
|
E:HIS98
|
3.2
|
28.4
|
1.0
|
CD2
|
C:HIS98
|
3.3
|
23.8
|
1.0
|
HD2
|
E:HIS98
|
3.4
|
34.1
|
1.0
|
HD2
|
C:HIS98
|
3.5
|
28.6
|
1.0
|
OE2
|
E:GLU71
|
4.0
|
57.8
|
1.0
|
OE2
|
C:GLU71
|
4.1
|
59.9
|
1.0
|
O
|
C:HOH602
|
4.2
|
32.7
|
1.0
|
O
|
E:HOH881
|
4.2
|
29.3
|
1.0
|
HG
|
E:SER67
|
4.2
|
47.1
|
1.0
|
ND1
|
E:HIS98
|
4.2
|
30.5
|
1.0
|
ND1
|
C:HIS98
|
4.2
|
26.4
|
1.0
|
OG
|
E:SER67
|
4.3
|
39.2
|
1.0
|
CG
|
E:HIS98
|
4.3
|
27.6
|
1.0
|
HG
|
C:SER67
|
4.3
|
60.3
|
1.0
|
CG
|
C:HIS98
|
4.4
|
26.9
|
1.0
|
HD11
|
E:LEU95
|
4.4
|
56.7
|
1.0
|
OE1
|
E:GLU71
|
4.5
|
44.8
|
1.0
|
OG
|
C:SER67
|
4.6
|
50.2
|
1.0
|
HD11
|
C:LEU95
|
4.6
|
44.5
|
1.0
|
CD
|
E:GLU71
|
4.7
|
50.2
|
1.0
|
HA2
|
E:GLY68
|
4.8
|
52.4
|
1.0
|
HA2
|
E:GLY64
|
4.8
|
51.1
|
1.0
|
HA2
|
C:GLY68
|
4.8
|
30.5
|
1.0
|
CD
|
C:GLU71
|
4.8
|
59.5
|
1.0
|
HD21
|
E:LEU95
|
4.9
|
54.2
|
1.0
|
OE1
|
C:GLU71
|
4.9
|
65.4
|
1.0
|
HD1
|
E:HIS98
|
5.0
|
36.6
|
1.0
|
HD21
|
C:LEU95
|
5.0
|
39.3
|
1.0
|
HD1
|
C:HIS98
|
5.0
|
31.7
|
1.0
|
|
Nickel binding site 3 out
of 3 in 4mgg
Go back to
Nickel Binding Sites List in 4mgg
Nickel binding site 3 out
of 3 in the Crystal Structure of An Enolase (Mandelate Racemase Subgroup) From Labrenzia Aggregata Iam 12614 (Target Nysgrc-012903) with Bound Mg, Space Group P212121
 Mono view
 Stereo pair view
|
A full contact list of Nickel with other atoms in the Ni binding
site number 3 of Crystal Structure of An Enolase (Mandelate Racemase Subgroup) From Labrenzia Aggregata Iam 12614 (Target Nysgrc-012903) with Bound Mg, Space Group P212121 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Ni401
b:28.1
occ:1.00
|
O
|
H:HOH502
|
1.9
|
14.0
|
1.0
|
O
|
H:HOH503
|
2.0
|
22.2
|
1.0
|
NE2
|
D:HIS98
|
2.0
|
32.9
|
1.0
|
O
|
D:HOH501
|
2.0
|
25.8
|
1.0
|
NE2
|
H:HIS98
|
2.0
|
28.1
|
1.0
|
O
|
H:HOH501
|
2.1
|
22.6
|
1.0
|
CE1
|
H:HIS98
|
2.9
|
27.6
|
1.0
|
CE1
|
D:HIS98
|
2.9
|
27.1
|
1.0
|
HE1
|
H:HIS98
|
3.0
|
33.2
|
1.0
|
HE1
|
D:HIS98
|
3.0
|
32.5
|
1.0
|
CD2
|
D:HIS98
|
3.1
|
30.2
|
1.0
|
CD2
|
H:HIS98
|
3.1
|
27.6
|
1.0
|
HD2
|
D:HIS98
|
3.4
|
36.2
|
1.0
|
HD2
|
H:HIS98
|
3.4
|
33.1
|
1.0
|
HG
|
H:SER67
|
3.7
|
44.1
|
1.0
|
OG
|
H:SER67
|
3.9
|
36.8
|
1.0
|
OE2
|
H:GLU71
|
4.0
|
45.4
|
1.0
|
HG
|
D:SER67
|
4.0
|
38.6
|
1.0
|
ND1
|
D:HIS98
|
4.1
|
25.9
|
1.0
|
ND1
|
H:HIS98
|
4.1
|
26.8
|
1.0
|
OG
|
D:SER67
|
4.1
|
32.1
|
1.0
|
O
|
D:HOH523
|
4.2
|
24.2
|
1.0
|
CG
|
D:HIS98
|
4.2
|
32.9
|
1.0
|
CG
|
H:HIS98
|
4.2
|
26.8
|
1.0
|
OE2
|
D:GLU71
|
4.3
|
47.8
|
1.0
|
OE1
|
D:GLU71
|
4.3
|
51.6
|
1.0
|
OE1
|
H:GLU71
|
4.4
|
40.2
|
1.0
|
O
|
D:HOH565
|
4.4
|
34.9
|
1.0
|
HD11
|
H:LEU95
|
4.4
|
33.2
|
1.0
|
HD11
|
D:LEU95
|
4.5
|
45.1
|
1.0
|
CD
|
H:GLU71
|
4.6
|
46.4
|
1.0
|
HA2
|
H:GLY68
|
4.7
|
34.6
|
1.0
|
CD
|
D:GLU71
|
4.7
|
48.6
|
1.0
|
HA2
|
H:GLY64
|
4.8
|
37.0
|
1.0
|
HA2
|
D:GLY64
|
4.8
|
33.9
|
1.0
|
HA2
|
D:GLY68
|
4.8
|
39.7
|
1.0
|
HD1
|
H:HIS98
|
4.8
|
32.2
|
1.0
|
HD1
|
D:HIS98
|
4.8
|
31.1
|
1.0
|
|
Reference:
M.W.Vetting,
X.Zhang,
S.R.Wasserman,
L.L.Morisco,
S.Sojitra,
J.B.Bonanno,
J.A.Gerlt,
S.C.Almo,
New York Structural Genomics Research Consortium (Nysgrc).
Crystal Structure of An Enolase (Mandelate Racemase Subgroup) From Labrenzia Aggregata Iam 12614 (Target Nysgrc-012903) with Bound Mg, Space Group P212121 To Be Published.
Page generated: Wed Oct 9 18:30:19 2024
|