Zinc in PDB 1h1o: Acidithiobacillus Ferrooxidans Cytochrome C4 Structure Supports A Complex-Induced Tuning of Electron Transfer
Protein crystallography data
The structure of Acidithiobacillus Ferrooxidans Cytochrome C4 Structure Supports A Complex-Induced Tuning of Electron Transfer, PDB code: 1h1o
was solved by
C.Abergel,
W.Nitschke,
G.Malarte,
M.Bruschi,
J.-M.Claverie,
M.-T.Guidici-Orticoni,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
25 /
2.13
|
Space group
|
P 64 2 2
|
Cell size a, b, c (Å), α, β, γ (°)
|
100.049,
100.049,
149.668,
90.00,
90.00,
120.00
|
R / Rfree (%)
|
23.9 /
28.4
|
Other elements in 1h1o:
The structure of Acidithiobacillus Ferrooxidans Cytochrome C4 Structure Supports A Complex-Induced Tuning of Electron Transfer also contains other interesting chemical elements:
Zinc Binding Sites:
The binding sites of Zinc atom in the Acidithiobacillus Ferrooxidans Cytochrome C4 Structure Supports A Complex-Induced Tuning of Electron Transfer
(pdb code 1h1o). This binding sites where shown within
5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the
Acidithiobacillus Ferrooxidans Cytochrome C4 Structure Supports A Complex-Induced Tuning of Electron Transfer, PDB code: 1h1o:
Jump to Zinc binding site number:
1;
2;
3;
4;
5;
6;
Zinc binding site 1 out
of 6 in 1h1o
Go back to
Zinc Binding Sites List in 1h1o
Zinc binding site 1 out
of 6 in the Acidithiobacillus Ferrooxidans Cytochrome C4 Structure Supports A Complex-Induced Tuning of Electron Transfer
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 1 of Acidithiobacillus Ferrooxidans Cytochrome C4 Structure Supports A Complex-Induced Tuning of Electron Transfer within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn1187
b:68.4
occ:1.00
|
O
|
A:HOH2114
|
2.7
|
78.4
|
1.0
|
O
|
A:HOH2115
|
3.0
|
90.4
|
0.5
|
NZ
|
A:LYS40
|
3.5
|
54.6
|
1.0
|
OD1
|
A:ASN84
|
3.6
|
48.3
|
1.0
|
ND1
|
A:HIS39
|
3.6
|
43.0
|
1.0
|
N
|
A:LYS40
|
3.8
|
42.8
|
1.0
|
ND2
|
A:ASN84
|
3.8
|
48.8
|
1.0
|
CA
|
A:HIS39
|
3.8
|
42.7
|
1.0
|
CB
|
A:HIS39
|
3.9
|
43.0
|
1.0
|
CG
|
A:ASN84
|
4.0
|
49.3
|
1.0
|
CG
|
A:HIS39
|
4.2
|
43.2
|
1.0
|
CE
|
A:LYS40
|
4.2
|
51.3
|
1.0
|
C
|
A:HIS39
|
4.3
|
42.8
|
1.0
|
CG
|
A:LYS40
|
4.4
|
47.4
|
1.0
|
CB
|
A:LYS40
|
4.6
|
44.2
|
1.0
|
O
|
A:HOH2001
|
4.6
|
54.5
|
1.0
|
CE1
|
A:HIS39
|
4.7
|
44.6
|
1.0
|
CA
|
A:LYS40
|
4.8
|
43.4
|
1.0
|
CD
|
A:LYS40
|
5.0
|
51.1
|
1.0
|
|
Zinc binding site 2 out
of 6 in 1h1o
Go back to
Zinc Binding Sites List in 1h1o
Zinc binding site 2 out
of 6 in the Acidithiobacillus Ferrooxidans Cytochrome C4 Structure Supports A Complex-Induced Tuning of Electron Transfer
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 2 of Acidithiobacillus Ferrooxidans Cytochrome C4 Structure Supports A Complex-Induced Tuning of Electron Transfer within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn1188
b:65.3
occ:1.00
|
O
|
A:HOH2084
|
3.3
|
37.7
|
1.0
|
N
|
A:TYR141
|
3.7
|
35.6
|
1.0
|
OG
|
A:SER93
|
3.7
|
60.7
|
1.0
|
NE2
|
A:HIS97
|
3.7
|
46.3
|
1.0
|
NH2
|
A:ARG34
|
3.7
|
34.5
|
1.0
|
NE
|
A:ARG140
|
4.0
|
38.3
|
1.0
|
NH2
|
A:ARG140
|
4.0
|
35.9
|
1.0
|
CB
|
A:TYR141
|
4.1
|
36.0
|
1.0
|
CD1
|
A:ILE95
|
4.1
|
63.4
|
1.0
|
CA
|
A:ARG140
|
4.2
|
35.0
|
1.0
|
CB
|
A:ARG140
|
4.4
|
34.7
|
1.0
|
C
|
A:ARG140
|
4.5
|
35.7
|
1.0
|
CZ
|
A:ARG140
|
4.5
|
37.8
|
1.0
|
CD2
|
A:HIS97
|
4.5
|
45.8
|
1.0
|
CB
|
A:SER93
|
4.5
|
59.7
|
1.0
|
CA
|
A:TYR141
|
4.6
|
36.0
|
1.0
|
CZ
|
A:ARG34
|
4.6
|
36.6
|
1.0
|
NH1
|
A:ARG34
|
4.6
|
36.9
|
1.0
|
CE1
|
A:HIS97
|
4.7
|
47.3
|
1.0
|
CB
|
A:ILE95
|
4.8
|
60.6
|
1.0
|
CG1
|
A:ILE95
|
4.8
|
62.6
|
1.0
|
CG
|
A:ARG140
|
4.9
|
36.0
|
1.0
|
CB
|
A:SER181
|
5.0
|
38.2
|
1.0
|
|
Zinc binding site 3 out
of 6 in 1h1o
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Zinc Binding Sites List in 1h1o
Zinc binding site 3 out
of 6 in the Acidithiobacillus Ferrooxidans Cytochrome C4 Structure Supports A Complex-Induced Tuning of Electron Transfer
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 3 of Acidithiobacillus Ferrooxidans Cytochrome C4 Structure Supports A Complex-Induced Tuning of Electron Transfer within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn1189
b:100.0
occ:1.00
|
NE2
|
A:HIS152
|
2.3
|
35.1
|
1.0
|
CD2
|
A:HIS152
|
3.2
|
33.4
|
1.0
|
CE1
|
A:HIS152
|
3.3
|
34.8
|
1.0
|
O
|
A:HOH2103
|
3.7
|
68.9
|
1.0
|
CG
|
A:HIS152
|
4.4
|
35.6
|
1.0
|
ND1
|
A:HIS152
|
4.4
|
35.9
|
1.0
|
O
|
A:HOH2091
|
4.4
|
62.4
|
1.0
|
O
|
A:HOH2104
|
4.7
|
57.7
|
1.0
|
|
Zinc binding site 4 out
of 6 in 1h1o
Go back to
Zinc Binding Sites List in 1h1o
Zinc binding site 4 out
of 6 in the Acidithiobacillus Ferrooxidans Cytochrome C4 Structure Supports A Complex-Induced Tuning of Electron Transfer
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 4 of Acidithiobacillus Ferrooxidans Cytochrome C4 Structure Supports A Complex-Induced Tuning of Electron Transfer within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Zn1388
b:36.3
occ:1.00
|
ND1
|
B:HIS239
|
2.1
|
29.4
|
1.0
|
OE1
|
A:GLU121
|
2.2
|
34.9
|
1.0
|
O1
|
B:SO41387
|
2.2
|
32.8
|
1.0
|
O
|
B:HOH2068
|
2.4
|
35.9
|
1.0
|
O4
|
B:SO41387
|
2.6
|
32.8
|
1.0
|
OE2
|
A:GLU121
|
2.6
|
30.4
|
1.0
|
CD
|
A:GLU121
|
2.7
|
30.7
|
1.0
|
S
|
B:SO41387
|
2.9
|
35.6
|
1.0
|
CE1
|
B:HIS239
|
3.0
|
29.0
|
1.0
|
CG
|
B:HIS239
|
3.1
|
29.6
|
1.0
|
CB
|
B:HIS239
|
3.4
|
32.5
|
1.0
|
CA
|
B:HIS239
|
3.6
|
34.6
|
1.0
|
ND2
|
B:ASN284
|
3.8
|
38.0
|
1.0
|
O3
|
B:SO41387
|
3.9
|
34.4
|
1.0
|
O2
|
B:SO41387
|
4.0
|
33.8
|
1.0
|
O
|
A:HOH2075
|
4.1
|
43.2
|
1.0
|
NE2
|
B:HIS239
|
4.1
|
29.7
|
1.0
|
CD2
|
B:HIS239
|
4.2
|
29.6
|
1.0
|
CG
|
A:GLU121
|
4.2
|
32.2
|
1.0
|
N
|
B:GLY331
|
4.4
|
32.5
|
1.0
|
N
|
B:LYS240
|
4.5
|
36.5
|
1.0
|
N
|
B:HIS239
|
4.6
|
34.0
|
1.0
|
O
|
B:HOH2067
|
4.6
|
33.3
|
1.0
|
C
|
B:HIS239
|
4.6
|
35.9
|
1.0
|
O
|
B:HOH2044
|
4.8
|
41.2
|
1.0
|
CA
|
B:ALA330
|
4.9
|
34.2
|
1.0
|
CG
|
B:ASN284
|
5.0
|
40.3
|
1.0
|
|
Zinc binding site 5 out
of 6 in 1h1o
Go back to
Zinc Binding Sites List in 1h1o
Zinc binding site 5 out
of 6 in the Acidithiobacillus Ferrooxidans Cytochrome C4 Structure Supports A Complex-Induced Tuning of Electron Transfer
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 5 of Acidithiobacillus Ferrooxidans Cytochrome C4 Structure Supports A Complex-Induced Tuning of Electron Transfer within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Zn1389
b:96.4
occ:1.00
|
NE2
|
B:HIS352
|
2.3
|
55.3
|
1.0
|
O
|
B:HOH2069
|
3.0
|
66.0
|
1.0
|
CD2
|
B:HIS352
|
3.1
|
54.0
|
1.0
|
O
|
B:HOH2070
|
3.3
|
71.5
|
1.0
|
CE1
|
B:HIS352
|
3.3
|
54.9
|
1.0
|
CG
|
B:HIS352
|
4.3
|
52.8
|
1.0
|
ND1
|
B:HIS352
|
4.3
|
54.5
|
1.0
|
O
|
B:HOH2009
|
4.4
|
60.8
|
1.0
|
O
|
B:HOH2071
|
4.4
|
64.1
|
1.0
|
|
Zinc binding site 6 out
of 6 in 1h1o
Go back to
Zinc Binding Sites List in 1h1o
Zinc binding site 6 out
of 6 in the Acidithiobacillus Ferrooxidans Cytochrome C4 Structure Supports A Complex-Induced Tuning of Electron Transfer
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 6 of Acidithiobacillus Ferrooxidans Cytochrome C4 Structure Supports A Complex-Induced Tuning of Electron Transfer within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Zn1390
b:79.0
occ:1.00
|
O
|
B:HOH2049
|
3.3
|
50.5
|
1.0
|
NH1
|
B:ARG234
|
3.5
|
40.5
|
1.0
|
NE2
|
B:HIS297
|
3.6
|
68.8
|
1.0
|
CD
|
B:ARG340
|
3.8
|
44.6
|
1.0
|
N
|
B:TYR341
|
4.0
|
38.5
|
1.0
|
NH1
|
B:ARG340
|
4.2
|
45.1
|
1.0
|
NH2
|
B:ARG234
|
4.2
|
42.5
|
1.0
|
CA
|
B:ARG340
|
4.2
|
38.1
|
1.0
|
CZ
|
B:ARG234
|
4.3
|
41.6
|
1.0
|
O
|
B:HOH2035
|
4.3
|
57.4
|
1.0
|
CD2
|
B:HIS297
|
4.3
|
69.1
|
1.0
|
NZ
|
B:LYS296
|
4.4
|
79.3
|
1.0
|
CB
|
B:TYR341
|
4.4
|
41.0
|
1.0
|
O
|
B:SER292
|
4.5
|
69.3
|
1.0
|
CB
|
B:ARG340
|
4.6
|
38.4
|
1.0
|
CE1
|
B:HIS297
|
4.6
|
68.7
|
1.0
|
C
|
B:ARG340
|
4.7
|
37.8
|
1.0
|
CG
|
B:ARG340
|
4.8
|
40.4
|
1.0
|
NE
|
B:ARG340
|
4.9
|
46.0
|
1.0
|
CA
|
B:TYR341
|
4.9
|
40.0
|
1.0
|
CB
|
B:SER381
|
4.9
|
42.8
|
1.0
|
|
Reference:
C.Abergel,
W.Nitschke,
G.Malarte,
M.Bruschi,
J.-M.Claverie,
M.-T.Guidici-Orticoni.
The Structure of Acidithiobacillus Ferrooxidans C(4)-Cytochrome. A Model For Complex-Induced Electron Transfer Tuning Structure V. 11 547 2003.
ISSN: ISSN 0969-2126
PubMed: 12737820
DOI: 10.1016/S0969-2126(03)00072-8
Page generated: Sun Oct 13 01:52:56 2024
|