Magnesium in PDB 8aln: Co-Bound [Fefe]-Hydrogenase I From Clostridium Pasteurianum (Cpi) at 1.34 Angstrom
Enzymatic activity of Co-Bound [Fefe]-Hydrogenase I From Clostridium Pasteurianum (Cpi) at 1.34 Angstrom
All present enzymatic activity of Co-Bound [Fefe]-Hydrogenase I From Clostridium Pasteurianum (Cpi) at 1.34 Angstrom:
1.12.7.2;
Protein crystallography data
The structure of Co-Bound [Fefe]-Hydrogenase I From Clostridium Pasteurianum (Cpi) at 1.34 Angstrom, PDB code: 8aln
was solved by
J.Duan,
E.Hofmann,
T.Happe,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
47.10 /
1.34
|
Space group
|
P 1 21 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
89.86,
71.85,
103.23,
90,
97.47,
90
|
R / Rfree (%)
|
14.9 /
17.5
|
Other elements in 8aln:
The structure of Co-Bound [Fefe]-Hydrogenase I From Clostridium Pasteurianum (Cpi) at 1.34 Angstrom also contains other interesting chemical elements:
Magnesium Binding Sites:
The binding sites of Magnesium atom in the Co-Bound [Fefe]-Hydrogenase I From Clostridium Pasteurianum (Cpi) at 1.34 Angstrom
(pdb code 8aln). This binding sites where shown within
5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the
Co-Bound [Fefe]-Hydrogenase I From Clostridium Pasteurianum (Cpi) at 1.34 Angstrom, PDB code: 8aln:
Jump to Magnesium binding site number:
1;
2;
3;
4;
5;
6;
Magnesium binding site 1 out
of 6 in 8aln
Go back to
Magnesium Binding Sites List in 8aln
Magnesium binding site 1 out
of 6 in the Co-Bound [Fefe]-Hydrogenase I From Clostridium Pasteurianum (Cpi) at 1.34 Angstrom
![](/pictures/MG/pdb/al/8aln-MG-sphere_01.jpg) Mono view
![](/pictures/MG/pdb/al/8aln-MG-sphere_01_stereo.jpg) Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 1 of Co-Bound [Fefe]-Hydrogenase I From Clostridium Pasteurianum (Cpi) at 1.34 Angstrom within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg607
b:28.5
occ:1.00
|
O
|
A:HOH985
|
2.0
|
32.1
|
1.0
|
O
|
A:HOH820
|
2.1
|
25.0
|
1.0
|
O
|
A:HOH952
|
2.1
|
27.1
|
1.0
|
O
|
A:HOH909
|
2.1
|
26.1
|
1.0
|
O
|
A:LEU218
|
2.1
|
26.7
|
1.0
|
O
|
A:HOH840
|
2.2
|
27.8
|
1.0
|
C
|
A:LEU218
|
3.2
|
26.3
|
1.0
|
CA
|
A:LEU218
|
3.8
|
25.6
|
1.0
|
O
|
A:HOH1208
|
4.0
|
46.0
|
1.0
|
O
|
A:ALA220
|
4.0
|
28.6
|
1.0
|
OD2
|
A:ASP263
|
4.0
|
28.3
|
1.0
|
O
|
A:HOH836
|
4.2
|
25.1
|
1.0
|
O
|
A:ALA217
|
4.2
|
24.9
|
1.0
|
O
|
A:LYS223
|
4.3
|
26.6
|
1.0
|
N
|
A:ASN219
|
4.3
|
26.8
|
1.0
|
OD1
|
A:ASP263
|
4.4
|
28.7
|
1.0
|
O
|
A:HOH757
|
4.6
|
42.9
|
1.0
|
CB
|
A:LEU218
|
4.6
|
24.4
|
1.0
|
O
|
A:GLY261
|
4.6
|
27.7
|
1.0
|
CG
|
A:ASP263
|
4.6
|
26.9
|
1.0
|
CA
|
A:ASN219
|
4.7
|
27.6
|
1.0
|
C
|
A:ASN219
|
4.8
|
28.7
|
1.0
|
N
|
A:ALA220
|
4.9
|
28.5
|
1.0
|
N
|
A:LEU218
|
4.9
|
25.1
|
1.0
|
C
|
A:ALA220
|
4.9
|
28.7
|
1.0
|
|
Magnesium binding site 2 out
of 6 in 8aln
Go back to
Magnesium Binding Sites List in 8aln
Magnesium binding site 2 out
of 6 in the Co-Bound [Fefe]-Hydrogenase I From Clostridium Pasteurianum (Cpi) at 1.34 Angstrom
![](/pictures/MG/pdb/al/8aln-MG-sphere_02.jpg) Mono view
![](/pictures/MG/pdb/al/8aln-MG-sphere_02_stereo.jpg) Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 2 of Co-Bound [Fefe]-Hydrogenase I From Clostridium Pasteurianum (Cpi) at 1.34 Angstrom within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg611
b:24.0
occ:1.00
|
OD1
|
A:ASP42
|
2.0
|
26.2
|
1.0
|
OD1
|
A:ASN40
|
2.0
|
22.7
|
1.0
|
O
|
A:HOH788
|
2.0
|
23.0
|
1.0
|
O
|
A:HOH998
|
2.1
|
23.7
|
1.0
|
O
|
A:HOH900
|
2.1
|
32.4
|
1.0
|
O
|
A:HOH971
|
2.1
|
26.4
|
1.0
|
CG
|
A:ASP42
|
3.1
|
27.4
|
1.0
|
CG
|
A:ASN40
|
3.2
|
21.1
|
1.0
|
OD2
|
A:ASP42
|
3.6
|
32.8
|
1.0
|
ND2
|
A:ASN40
|
3.9
|
21.1
|
1.0
|
O
|
A:HOH704
|
3.9
|
31.2
|
1.0
|
N
|
A:ASN40
|
4.0
|
22.5
|
1.0
|
O
|
A:ASN40
|
4.2
|
23.2
|
1.0
|
O
|
B:HOH785
|
4.2
|
26.6
|
1.0
|
OD2
|
A:ASP63
|
4.3
|
23.9
|
1.0
|
O
|
A:HOH1062
|
4.3
|
43.9
|
1.0
|
OD1
|
B:ASN452
|
4.3
|
30.3
|
1.0
|
CB
|
A:ASP42
|
4.4
|
25.3
|
1.0
|
CB
|
A:ASN40
|
4.4
|
21.5
|
1.0
|
CB
|
A:ASP63
|
4.4
|
22.8
|
1.0
|
C
|
A:ASN40
|
4.5
|
21.6
|
1.0
|
CA
|
A:ASN40
|
4.5
|
22.0
|
1.0
|
CG
|
B:ASN452
|
4.5
|
26.0
|
1.0
|
CA
|
A:ASP42
|
4.6
|
23.7
|
1.0
|
O
|
B:HOH1056
|
4.8
|
30.0
|
1.0
|
N
|
A:ASP42
|
4.8
|
22.4
|
1.0
|
CB
|
B:ASN452
|
4.8
|
22.2
|
1.0
|
CG
|
A:ASP63
|
4.9
|
23.4
|
1.0
|
|
Magnesium binding site 3 out
of 6 in 8aln
Go back to
Magnesium Binding Sites List in 8aln
Magnesium binding site 3 out
of 6 in the Co-Bound [Fefe]-Hydrogenase I From Clostridium Pasteurianum (Cpi) at 1.34 Angstrom
![](/pictures/MG/pdb/al/8aln-MG-sphere_03.jpg) Mono view
![](/pictures/MG/pdb/al/8aln-MG-sphere_03_stereo.jpg) Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 3 of Co-Bound [Fefe]-Hydrogenase I From Clostridium Pasteurianum (Cpi) at 1.34 Angstrom within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg612
b:58.7
occ:1.00
|
O
|
A:HOH1055
|
2.0
|
52.6
|
1.0
|
O
|
A:HOH940
|
2.1
|
48.5
|
1.0
|
O
|
A:HOH1090
|
2.1
|
64.5
|
1.0
|
NE2
|
A:HIS565
|
2.1
|
47.8
|
1.0
|
OG
|
A:SER320
|
2.2
|
32.1
|
1.0
|
O
|
A:HOH710
|
3.0
|
58.1
|
1.0
|
CE1
|
A:HIS565
|
3.1
|
47.5
|
1.0
|
CD2
|
A:HIS565
|
3.2
|
46.9
|
1.0
|
CB
|
A:SER320
|
3.3
|
29.6
|
1.0
|
ND1
|
A:HIS569
|
4.0
|
31.1
|
1.0
|
O
|
A:HOH835
|
4.0
|
34.4
|
1.0
|
OE2
|
A:GLU282
|
4.1
|
42.4
|
1.0
|
ND1
|
A:HIS565
|
4.2
|
47.7
|
1.0
|
CD
|
A:GLU282
|
4.3
|
40.1
|
1.0
|
CG
|
A:HIS565
|
4.3
|
46.3
|
1.0
|
CE1
|
A:HIS569
|
4.5
|
31.1
|
1.0
|
OE1
|
A:GLU282
|
4.5
|
39.1
|
1.0
|
CA
|
A:SER320
|
4.6
|
27.8
|
1.0
|
N
|
A:SER320
|
4.7
|
27.7
|
1.0
|
CG
|
A:HIS569
|
4.8
|
30.3
|
1.0
|
|
Magnesium binding site 4 out
of 6 in 8aln
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Magnesium Binding Sites List in 8aln
Magnesium binding site 4 out
of 6 in the Co-Bound [Fefe]-Hydrogenase I From Clostridium Pasteurianum (Cpi) at 1.34 Angstrom
![](/pictures/MG/pdb/al/8aln-MG-sphere_04.jpg) Mono view
![](/pictures/MG/pdb/al/8aln-MG-sphere_04_stereo.jpg) Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 4 of Co-Bound [Fefe]-Hydrogenase I From Clostridium Pasteurianum (Cpi) at 1.34 Angstrom within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg607
b:27.4
occ:1.00
|
O
|
B:HOH867
|
2.1
|
24.2
|
1.0
|
O
|
B:HOH1010
|
2.1
|
29.9
|
1.0
|
O
|
B:HOH825
|
2.1
|
23.2
|
1.0
|
O
|
B:HOH856
|
2.1
|
26.7
|
1.0
|
O
|
B:HOH945
|
2.1
|
26.1
|
1.0
|
O
|
B:LEU218
|
2.2
|
27.4
|
1.0
|
C
|
B:LEU218
|
3.2
|
24.8
|
1.0
|
CA
|
B:LEU218
|
3.8
|
23.1
|
1.0
|
OD2
|
B:ASP263
|
4.0
|
24.6
|
1.0
|
O
|
B:ALA220
|
4.1
|
28.2
|
1.0
|
O
|
B:HOH1232
|
4.1
|
43.1
|
1.0
|
O
|
B:HOH842
|
4.2
|
24.7
|
1.0
|
OD1
|
B:ASP263
|
4.3
|
25.4
|
1.0
|
O
|
B:ALA217
|
4.3
|
23.3
|
1.0
|
O
|
B:LYS223
|
4.3
|
26.1
|
1.0
|
N
|
B:ASN219
|
4.4
|
26.6
|
1.0
|
O
|
B:GLY261
|
4.5
|
25.4
|
1.0
|
CG
|
B:ASP263
|
4.6
|
23.0
|
1.0
|
CB
|
B:LEU218
|
4.6
|
23.3
|
1.0
|
CA
|
B:ASN219
|
4.7
|
28.9
|
1.0
|
O
|
B:HOH1146
|
4.8
|
56.7
|
1.0
|
C
|
B:ASN219
|
4.9
|
29.2
|
1.0
|
N
|
B:LEU218
|
4.9
|
24.3
|
1.0
|
N
|
B:ALA220
|
4.9
|
27.3
|
1.0
|
C
|
B:ALA220
|
5.0
|
27.9
|
1.0
|
|
Magnesium binding site 5 out
of 6 in 8aln
Go back to
Magnesium Binding Sites List in 8aln
Magnesium binding site 5 out
of 6 in the Co-Bound [Fefe]-Hydrogenase I From Clostridium Pasteurianum (Cpi) at 1.34 Angstrom
![](/pictures/MG/pdb/al/8aln-MG-sphere_05.jpg) Mono view
![](/pictures/MG/pdb/al/8aln-MG-sphere_05_stereo.jpg) Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 5 of Co-Bound [Fefe]-Hydrogenase I From Clostridium Pasteurianum (Cpi) at 1.34 Angstrom within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg610
b:32.5
occ:1.00
|
OD1
|
B:ASN40
|
1.9
|
32.4
|
1.0
|
O
|
B:HOH1077
|
2.0
|
33.3
|
1.0
|
O
|
B:HOH1067
|
2.1
|
31.5
|
1.0
|
O
|
B:HOH713
|
2.1
|
32.9
|
1.0
|
O
|
B:HOH824
|
2.1
|
31.0
|
1.0
|
OD1
|
B:ASP42
|
2.2
|
41.5
|
1.0
|
CG
|
B:ASN40
|
3.0
|
31.6
|
1.0
|
CG
|
B:ASP42
|
3.3
|
42.1
|
1.0
|
ND2
|
B:ASN40
|
3.6
|
33.8
|
1.0
|
OD2
|
B:ASP42
|
3.7
|
43.1
|
1.0
|
O
|
B:HOH1138
|
3.7
|
49.9
|
1.0
|
N
|
B:ASN40
|
3.9
|
27.6
|
1.0
|
O
|
B:HOH721
|
4.1
|
30.4
|
1.0
|
OD2
|
B:ASP63
|
4.1
|
38.0
|
1.0
|
CB
|
B:ASN40
|
4.3
|
29.1
|
1.0
|
O
|
A:HOH881
|
4.3
|
29.0
|
1.0
|
OD1
|
A:ASN452
|
4.3
|
37.5
|
1.0
|
O
|
B:ASN40
|
4.4
|
27.5
|
1.0
|
CG
|
A:ASN452
|
4.5
|
32.8
|
1.0
|
CA
|
B:ASN40
|
4.5
|
27.7
|
1.0
|
CB
|
B:ASP63
|
4.5
|
37.1
|
1.0
|
CB
|
B:ASP42
|
4.6
|
39.6
|
1.0
|
C
|
B:ASN40
|
4.6
|
26.5
|
1.0
|
CG
|
B:ASP63
|
4.8
|
37.8
|
1.0
|
ND2
|
A:ASN452
|
4.8
|
33.4
|
1.0
|
CA
|
B:ASP42
|
4.9
|
36.4
|
1.0
|
CB
|
A:ASN452
|
4.9
|
27.9
|
1.0
|
|
Magnesium binding site 6 out
of 6 in 8aln
Go back to
Magnesium Binding Sites List in 8aln
Magnesium binding site 6 out
of 6 in the Co-Bound [Fefe]-Hydrogenase I From Clostridium Pasteurianum (Cpi) at 1.34 Angstrom
![](/pictures/MG/pdb/al/8aln-MG-sphere_06.jpg) Mono view
![](/pictures/MG/pdb/al/8aln-MG-sphere_06_stereo.jpg) Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 6 of Co-Bound [Fefe]-Hydrogenase I From Clostridium Pasteurianum (Cpi) at 1.34 Angstrom within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg611
b:58.4
occ:1.00
|
O
|
B:HOH895
|
2.1
|
32.5
|
1.0
|
O
|
B:HOH799
|
2.1
|
35.0
|
1.0
|
O
|
B:HOH1261
|
2.2
|
51.7
|
1.0
|
O
|
B:HOH974
|
2.2
|
28.0
|
1.0
|
O
|
B:HOH782
|
3.9
|
49.5
|
1.0
|
OD1
|
B:ASN309
|
4.0
|
24.6
|
1.0
|
O
|
B:ASP187
|
4.2
|
25.6
|
1.0
|
O
|
B:THR188
|
4.3
|
21.2
|
1.0
|
OD1
|
B:ASN189
|
4.4
|
28.4
|
1.0
|
C
|
B:THR188
|
4.6
|
19.5
|
1.0
|
C
|
B:ASP187
|
4.7
|
22.8
|
1.0
|
CG
|
B:ASN309
|
4.7
|
23.2
|
1.0
|
O
|
B:HOH944
|
4.8
|
45.7
|
1.0
|
O
|
B:HOH1230
|
4.9
|
54.9
|
1.0
|
CA
|
B:THR188
|
4.9
|
20.8
|
1.0
|
|
Reference:
J.Duan,
A.Hemschemeier,
D.J.Burr,
S.T.Stripp,
E.Hofmann,
T.Happe.
Cyanide Binding to [Fefe]-Hydrogenase Stabilizes the Alternative Configuration of the Proton Transfer Pathway. Angew.Chem.Int.Ed.Engl. 2022.
ISSN: ESSN 1521-3773
PubMed: 36464641
DOI: 10.1002/ANIE.202216903
Page generated: Fri Apr 7 06:06:34 2023
|