Iron in PDB 1m2a: Crystal Structure at 1.5 Angstroms Resolution of the Wild Type Thioredoxin-Like [2FE-2S] Ferredoxin From Aquifex Aeolicus
Protein crystallography data
The structure of Crystal Structure at 1.5 Angstroms Resolution of the Wild Type Thioredoxin-Like [2FE-2S] Ferredoxin From Aquifex Aeolicus, PDB code: 1m2a
was solved by
A.P.Yeh,
X.I.Ambroggio,
S.L.A.Andrade,
O.Einsle,
C.Chatelet,
J.Meyer,
D.C.Rees,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
31.50 /
1.50
|
Space group
|
C 1 2 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
67.200,
59.800,
47.200,
90.00,
110.30,
90.00
|
R / Rfree (%)
|
18.4 /
21.6
|
Other elements in 1m2a:
The structure of Crystal Structure at 1.5 Angstroms Resolution of the Wild Type Thioredoxin-Like [2FE-2S] Ferredoxin From Aquifex Aeolicus also contains other interesting chemical elements:
Iron Binding Sites:
The binding sites of Iron atom in the Crystal Structure at 1.5 Angstroms Resolution of the Wild Type Thioredoxin-Like [2FE-2S] Ferredoxin From Aquifex Aeolicus
(pdb code 1m2a). This binding sites where shown within
5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the
Crystal Structure at 1.5 Angstroms Resolution of the Wild Type Thioredoxin-Like [2FE-2S] Ferredoxin From Aquifex Aeolicus, PDB code: 1m2a:
Jump to Iron binding site number:
1;
2;
3;
4;
Iron binding site 1 out
of 4 in 1m2a
Go back to
Iron Binding Sites List in 1m2a
Iron binding site 1 out
of 4 in the Crystal Structure at 1.5 Angstroms Resolution of the Wild Type Thioredoxin-Like [2FE-2S] Ferredoxin From Aquifex Aeolicus
 Mono view
 Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 1 of Crystal Structure at 1.5 Angstroms Resolution of the Wild Type Thioredoxin-Like [2FE-2S] Ferredoxin From Aquifex Aeolicus within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe201
b:12.2
occ:1.00
|
FE1
|
A:FES201
|
0.0
|
12.2
|
1.0
|
S2
|
A:FES201
|
2.2
|
12.9
|
1.0
|
S1
|
A:FES201
|
2.2
|
13.3
|
1.0
|
SG
|
A:CYS9
|
2.3
|
11.5
|
1.0
|
SG
|
A:CYS22
|
2.3
|
12.9
|
1.0
|
FE2
|
A:FES201
|
2.7
|
13.5
|
1.0
|
CB
|
A:CYS22
|
3.3
|
12.3
|
1.0
|
CB
|
A:CYS9
|
3.3
|
8.8
|
1.0
|
N
|
A:CYS22
|
3.9
|
12.7
|
1.0
|
CA
|
A:CYS55
|
4.1
|
11.6
|
1.0
|
CA
|
A:CYS22
|
4.2
|
12.7
|
1.0
|
O
|
A:HOH318
|
4.3
|
18.9
|
1.0
|
N
|
A:MET56
|
4.4
|
11.5
|
1.0
|
CB
|
A:GLN11
|
4.5
|
13.6
|
1.0
|
SG
|
A:CYS55
|
4.6
|
14.3
|
1.0
|
CA
|
A:CYS9
|
4.6
|
9.5
|
1.0
|
CG2
|
A:VAL64
|
4.7
|
13.6
|
1.0
|
CB
|
A:CYS55
|
4.7
|
13.9
|
1.0
|
SG
|
A:CYS59
|
4.7
|
15.3
|
1.0
|
C
|
A:CYS55
|
4.8
|
12.8
|
1.0
|
CB
|
A:VAL64
|
4.8
|
9.3
|
1.0
|
CA
|
A:CYS59
|
4.9
|
13.6
|
1.0
|
C
|
A:CYS9
|
4.9
|
11.1
|
1.0
|
N
|
A:CYS55
|
4.9
|
12.8
|
1.0
|
C
|
A:SER21
|
4.9
|
18.3
|
1.0
|
O
|
A:CYS9
|
5.0
|
11.0
|
1.0
|
|
Iron binding site 2 out
of 4 in 1m2a
Go back to
Iron Binding Sites List in 1m2a
Iron binding site 2 out
of 4 in the Crystal Structure at 1.5 Angstroms Resolution of the Wild Type Thioredoxin-Like [2FE-2S] Ferredoxin From Aquifex Aeolicus
 Mono view
 Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 2 of Crystal Structure at 1.5 Angstroms Resolution of the Wild Type Thioredoxin-Like [2FE-2S] Ferredoxin From Aquifex Aeolicus within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe201
b:13.5
occ:1.00
|
FE2
|
A:FES201
|
0.0
|
13.5
|
1.0
|
S1
|
A:FES201
|
2.2
|
13.3
|
1.0
|
S2
|
A:FES201
|
2.2
|
12.9
|
1.0
|
SG
|
A:CYS59
|
2.3
|
15.3
|
1.0
|
SG
|
A:CYS55
|
2.3
|
14.3
|
1.0
|
FE1
|
A:FES201
|
2.7
|
12.2
|
1.0
|
CB
|
A:CYS55
|
3.4
|
13.9
|
1.0
|
CB
|
A:CYS59
|
3.4
|
18.4
|
1.0
|
CA
|
A:CYS55
|
3.7
|
11.6
|
1.0
|
CA
|
A:CYS59
|
3.7
|
13.6
|
1.0
|
N
|
A:CYS59
|
3.9
|
16.6
|
1.0
|
NH1
|
A:ARG13
|
4.0
|
17.6
|
1.0
|
N
|
A:ASN57
|
4.0
|
14.3
|
1.0
|
N
|
A:MET56
|
4.0
|
11.5
|
1.0
|
NH2
|
A:ARG13
|
4.1
|
27.5
|
1.0
|
C
|
A:CYS55
|
4.3
|
12.8
|
1.0
|
N
|
A:ALA58
|
4.3
|
15.6
|
1.0
|
SG
|
A:CYS9
|
4.4
|
11.5
|
1.0
|
CZ
|
A:ARG13
|
4.4
|
25.9
|
1.0
|
CA
|
A:ASN57
|
4.5
|
16.2
|
1.0
|
SG
|
A:CYS22
|
4.6
|
12.9
|
1.0
|
C
|
A:ALA58
|
4.7
|
11.9
|
1.0
|
C
|
A:ASN57
|
4.8
|
18.6
|
1.0
|
C
|
A:MET56
|
4.9
|
14.9
|
1.0
|
N
|
A:CYS55
|
4.9
|
12.8
|
1.0
|
|
Iron binding site 3 out
of 4 in 1m2a
Go back to
Iron Binding Sites List in 1m2a
Iron binding site 3 out
of 4 in the Crystal Structure at 1.5 Angstroms Resolution of the Wild Type Thioredoxin-Like [2FE-2S] Ferredoxin From Aquifex Aeolicus
 Mono view
 Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 3 of Crystal Structure at 1.5 Angstroms Resolution of the Wild Type Thioredoxin-Like [2FE-2S] Ferredoxin From Aquifex Aeolicus within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Fe202
b:12.0
occ:1.00
|
FE1
|
B:FES202
|
0.0
|
12.0
|
1.0
|
S2
|
B:FES202
|
2.2
|
12.7
|
1.0
|
S1
|
B:FES202
|
2.2
|
13.3
|
1.0
|
SG
|
B:CYS9
|
2.3
|
11.1
|
1.0
|
SG
|
B:CYS22
|
2.3
|
11.5
|
1.0
|
FE2
|
B:FES202
|
2.7
|
13.3
|
1.0
|
CB
|
B:CYS22
|
3.2
|
11.2
|
1.0
|
CB
|
B:CYS9
|
3.3
|
8.7
|
1.0
|
N
|
B:CYS22
|
3.9
|
11.4
|
1.0
|
CA
|
B:CYS55
|
4.1
|
11.8
|
1.0
|
CA
|
B:CYS22
|
4.2
|
11.1
|
1.0
|
O
|
B:HOH431
|
4.2
|
18.6
|
1.0
|
N
|
B:MET56
|
4.4
|
11.2
|
1.0
|
CB
|
B:GLN11
|
4.4
|
12.4
|
1.0
|
SG
|
B:CYS55
|
4.6
|
14.1
|
1.0
|
CA
|
B:CYS9
|
4.6
|
8.6
|
1.0
|
CB
|
B:CYS55
|
4.7
|
11.5
|
1.0
|
CG2
|
B:VAL64
|
4.7
|
11.2
|
1.0
|
SG
|
B:CYS59
|
4.8
|
16.2
|
1.0
|
CA
|
B:CYS59
|
4.8
|
13.9
|
1.0
|
C
|
B:CYS55
|
4.8
|
11.5
|
1.0
|
CB
|
B:VAL64
|
4.9
|
10.0
|
1.0
|
C
|
B:CYS9
|
4.9
|
12.2
|
1.0
|
N
|
B:CYS55
|
5.0
|
11.2
|
1.0
|
O
|
B:CYS9
|
5.0
|
11.6
|
1.0
|
C
|
B:SER21
|
5.0
|
14.2
|
1.0
|
|
Iron binding site 4 out
of 4 in 1m2a
Go back to
Iron Binding Sites List in 1m2a
Iron binding site 4 out
of 4 in the Crystal Structure at 1.5 Angstroms Resolution of the Wild Type Thioredoxin-Like [2FE-2S] Ferredoxin From Aquifex Aeolicus
 Mono view
 Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 4 of Crystal Structure at 1.5 Angstroms Resolution of the Wild Type Thioredoxin-Like [2FE-2S] Ferredoxin From Aquifex Aeolicus within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Fe202
b:13.3
occ:1.00
|
FE2
|
B:FES202
|
0.0
|
13.3
|
1.0
|
S1
|
B:FES202
|
2.2
|
13.3
|
1.0
|
S2
|
B:FES202
|
2.3
|
12.7
|
1.0
|
SG
|
B:CYS59
|
2.3
|
16.2
|
1.0
|
SG
|
B:CYS55
|
2.4
|
14.1
|
1.0
|
FE1
|
B:FES202
|
2.7
|
12.0
|
1.0
|
CB
|
B:CYS55
|
3.4
|
11.5
|
1.0
|
CB
|
B:CYS59
|
3.4
|
14.3
|
1.0
|
CA
|
B:CYS55
|
3.7
|
11.8
|
1.0
|
CA
|
B:CYS59
|
3.7
|
13.9
|
1.0
|
NH1
|
B:ARG13
|
3.9
|
8.0
|
0.5
|
N
|
B:CYS59
|
3.9
|
13.7
|
1.0
|
NH2
|
B:ARG13
|
3.9
|
21.9
|
0.5
|
N
|
B:MET56
|
4.0
|
11.2
|
1.0
|
N
|
B:ASN57
|
4.0
|
14.1
|
1.0
|
N
|
B:ALA58
|
4.3
|
16.1
|
1.0
|
C
|
B:CYS55
|
4.3
|
11.5
|
1.0
|
CZ
|
B:ARG13
|
4.3
|
20.5
|
0.5
|
SG
|
B:CYS9
|
4.4
|
11.1
|
1.0
|
CA
|
B:ASN57
|
4.5
|
16.8
|
1.0
|
SG
|
B:CYS22
|
4.6
|
11.5
|
1.0
|
C
|
B:ALA58
|
4.7
|
15.0
|
1.0
|
C
|
B:ASN57
|
4.9
|
21.9
|
1.0
|
C
|
B:MET56
|
4.9
|
13.9
|
1.0
|
N
|
B:CYS55
|
5.0
|
11.2
|
1.0
|
O
|
B:HOH431
|
5.0
|
18.6
|
1.0
|
|
Reference:
A.P.Yeh,
X.I.Ambroggio,
S.L.A.Andrade,
O.Einsle,
C.Chatelet,
J.Meyer,
D.C.Rees.
High-Resolution Crystal Structures of the Wild Type and Cys-55-->Ser and Cys-59-->Ser Variants of the Thioredoxin-Like [2FE-2S] Ferredoxin From Aquifex Aeolicus J.Biol.Chem. V. 277 34499 2002.
ISSN: ISSN 0021-9258
PubMed: 12089152
DOI: 10.1074/JBC.M205096200
Page generated: Sat Aug 3 09:58:39 2024
|