Iron in PDB 3tbn: Crystal Structure of A MINER2 Homolog: A Type 6 Cdgsh Iron-Sulfur Protein.
Protein crystallography data
The structure of Crystal Structure of A MINER2 Homolog: A Type 6 Cdgsh Iron-Sulfur Protein., PDB code: 3tbn
was solved by
J.Lin,
L.Zhang,
K.Ye,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
14.06 /
1.15
|
Space group
|
P 65
|
Cell size a, b, c (Å), α, β, γ (°)
|
63.498,
63.498,
49.068,
90.00,
90.00,
120.00
|
R / Rfree (%)
|
11.1 /
12.5
|
Iron Binding Sites:
The binding sites of Iron atom in the Crystal Structure of A MINER2 Homolog: A Type 6 Cdgsh Iron-Sulfur Protein.
(pdb code 3tbn). 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 of A MINER2 Homolog: A Type 6 Cdgsh Iron-Sulfur Protein., PDB code: 3tbn:
Jump to Iron binding site number:
1;
2;
3;
4;
Iron binding site 1 out
of 4 in 3tbn
Go back to
Iron Binding Sites List in 3tbn
Iron binding site 1 out
of 4 in the Crystal Structure of A MINER2 Homolog: A Type 6 Cdgsh Iron-Sulfur Protein.
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 1 of Crystal Structure of A MINER2 Homolog: A Type 6 Cdgsh Iron-Sulfur Protein. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe80
b:6.5
occ:0.88
|
FE1
|
A:FES80
|
0.0
|
6.5
|
0.9
|
ND1
|
A:HIS40
|
2.1
|
7.4
|
0.9
|
S1
|
A:FES80
|
2.2
|
6.8
|
0.9
|
S2
|
A:FES80
|
2.2
|
6.6
|
0.9
|
SG
|
A:CYS36
|
2.3
|
7.4
|
0.9
|
FE2
|
A:FES80
|
2.7
|
5.7
|
0.9
|
HB3
|
A:HIS40
|
2.9
|
10.1
|
1.0
|
CE1
|
A:HIS40
|
3.1
|
10.0
|
1.0
|
CG
|
A:HIS40
|
3.2
|
7.9
|
0.9
|
H
|
A:HIS40
|
3.2
|
9.2
|
0.6
|
HE1
|
A:HIS40
|
3.2
|
12.0
|
1.0
|
HB2
|
A:CYS36
|
3.2
|
9.5
|
1.0
|
H
|
A:GLY38
|
3.2
|
10.0
|
0.5
|
HA
|
A:CYS36
|
3.3
|
8.1
|
1.0
|
CB
|
A:CYS36
|
3.3
|
7.9
|
1.0
|
HD3
|
A:PRO47
|
3.4
|
14.3
|
1.0
|
CB
|
A:HIS40
|
3.5
|
8.4
|
1.0
|
HB3
|
A:PRO47
|
3.6
|
14.4
|
1.0
|
CA
|
A:CYS36
|
3.8
|
6.8
|
1.0
|
H
|
A:ASP37
|
3.8
|
9.0
|
0.7
|
HA
|
A:CYS25
|
3.9
|
7.2
|
1.0
|
N
|
A:HIS40
|
3.9
|
7.6
|
0.9
|
N
|
A:GLY38
|
4.0
|
8.4
|
1.0
|
HA2
|
A:GLY38
|
4.0
|
11.6
|
0.9
|
HB3
|
A:CYS36
|
4.2
|
9.5
|
0.9
|
H
|
A:SER39
|
4.2
|
9.4
|
0.7
|
NE2
|
A:HIS40
|
4.2
|
10.6
|
0.9
|
CD
|
A:PRO47
|
4.2
|
11.9
|
1.0
|
HG3
|
A:PRO47
|
4.2
|
15.6
|
0.7
|
N
|
A:ASP37
|
4.2
|
7.5
|
1.0
|
CD2
|
A:HIS40
|
4.3
|
10.6
|
0.9
|
HB2
|
A:HIS40
|
4.3
|
10.1
|
1.0
|
CA
|
A:HIS40
|
4.3
|
7.6
|
1.0
|
CA
|
A:GLY38
|
4.4
|
9.7
|
0.9
|
N
|
A:SER39
|
4.4
|
7.9
|
0.9
|
C
|
A:CYS36
|
4.4
|
7.2
|
0.9
|
CB
|
A:PRO47
|
4.4
|
12.0
|
1.0
|
SG
|
A:CYS27
|
4.5
|
6.5
|
0.9
|
CG
|
A:PRO47
|
4.5
|
13.0
|
1.0
|
C
|
A:GLY38
|
4.5
|
8.7
|
0.9
|
HB2
|
A:CYS25
|
4.6
|
7.6
|
1.0
|
HB2
|
A:SER30
|
4.6
|
8.5
|
1.0
|
N
|
A:PRO47
|
4.7
|
8.9
|
0.9
|
SG
|
A:CYS25
|
4.7
|
5.9
|
0.9
|
H
|
A:ALA26
|
4.7
|
7.7
|
1.0
|
HA
|
A:PRO47
|
4.7
|
11.0
|
0.9
|
CA
|
A:CYS25
|
4.8
|
6.0
|
1.0
|
HA
|
A:HIS40
|
4.8
|
9.1
|
0.8
|
HA
|
A:ALA46
|
4.9
|
13.9
|
1.0
|
CB
|
A:CYS25
|
4.9
|
6.3
|
0.9
|
CA
|
A:PRO47
|
4.9
|
9.1
|
0.9
|
HE2
|
A:HIS40
|
5.0
|
12.7
|
1.0
|
HD2
|
A:PRO47
|
5.0
|
14.3
|
1.0
|
H
|
A:CYS27
|
5.0
|
8.2
|
0.5
|
|
Iron binding site 2 out
of 4 in 3tbn
Go back to
Iron Binding Sites List in 3tbn
Iron binding site 2 out
of 4 in the Crystal Structure of A MINER2 Homolog: A Type 6 Cdgsh Iron-Sulfur Protein.
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 2 of Crystal Structure of A MINER2 Homolog: A Type 6 Cdgsh Iron-Sulfur Protein. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe80
b:5.7
occ:0.87
|
FE2
|
A:FES80
|
0.0
|
5.7
|
0.9
|
S1
|
A:FES80
|
2.2
|
6.8
|
0.9
|
S2
|
A:FES80
|
2.2
|
6.6
|
0.9
|
SG
|
A:CYS27
|
2.4
|
6.5
|
0.9
|
SG
|
A:CYS25
|
2.4
|
5.9
|
0.9
|
FE1
|
A:FES80
|
2.7
|
6.5
|
0.9
|
H
|
A:CYS27
|
2.8
|
8.2
|
0.5
|
HB3
|
A:HIS40
|
3.1
|
10.1
|
1.0
|
HA
|
A:CYS25
|
3.2
|
7.2
|
1.0
|
CB
|
A:CYS25
|
3.4
|
6.3
|
0.9
|
HB2
|
A:CYS25
|
3.5
|
7.6
|
1.0
|
CB
|
A:CYS27
|
3.5
|
7.2
|
1.0
|
HB3
|
A:CYS27
|
3.5
|
8.7
|
1.0
|
H
|
A:SER30
|
3.6
|
8.2
|
1.0
|
H
|
A:ARG29
|
3.6
|
7.6
|
0.2
|
N
|
A:CYS27
|
3.6
|
6.8
|
0.9
|
HB2
|
A:SER30
|
3.7
|
8.5
|
1.0
|
CA
|
A:CYS25
|
3.7
|
6.0
|
1.0
|
H
|
A:ALA26
|
3.7
|
7.7
|
1.0
|
HA
|
A:CYS36
|
3.8
|
8.1
|
1.0
|
H
|
A:GLY28
|
3.8
|
7.7
|
1.0
|
H
|
A:HIS40
|
3.9
|
9.2
|
0.6
|
CB
|
A:HIS40
|
4.0
|
8.4
|
1.0
|
N
|
A:ALA26
|
4.0
|
6.4
|
1.0
|
CA
|
A:CYS27
|
4.0
|
6.6
|
1.0
|
HB2
|
A:ARG29
|
4.1
|
9.3
|
1.0
|
C
|
A:CYS25
|
4.1
|
5.9
|
0.9
|
N
|
A:SER30
|
4.3
|
6.8
|
0.9
|
HB3
|
A:CYS25
|
4.3
|
7.6
|
1.0
|
N
|
A:GLY28
|
4.3
|
6.4
|
0.9
|
N
|
A:HIS40
|
4.3
|
7.6
|
0.9
|
ND1
|
A:HIS40
|
4.3
|
7.4
|
0.9
|
HB2
|
A:CYS27
|
4.3
|
8.7
|
1.0
|
N
|
A:ARG29
|
4.4
|
6.4
|
0.9
|
HA
|
A:HIS40
|
4.4
|
9.1
|
0.8
|
CB
|
A:SER30
|
4.5
|
7.1
|
1.0
|
CA
|
A:HIS40
|
4.5
|
7.6
|
1.0
|
HB2
|
A:SER39
|
4.5
|
13.3
|
1.0
|
C
|
A:CYS27
|
4.5
|
6.1
|
0.9
|
HB2
|
A:CYS36
|
4.5
|
9.5
|
1.0
|
HB3
|
A:SER30
|
4.6
|
8.5
|
1.0
|
H
|
A:ASP37
|
4.6
|
9.0
|
0.7
|
HB2
|
A:HIS40
|
4.6
|
10.1
|
1.0
|
CG
|
A:HIS40
|
4.6
|
7.9
|
0.9
|
CA
|
A:CYS36
|
4.7
|
6.8
|
1.0
|
SG
|
A:CYS36
|
4.7
|
7.4
|
0.9
|
C
|
A:ALA26
|
4.7
|
6.1
|
0.9
|
HE21
|
A:GLN33
|
4.8
|
9.2
|
0.5
|
CB
|
A:CYS36
|
4.9
|
7.9
|
1.0
|
CA
|
A:SER30
|
4.9
|
7.0
|
1.0
|
H
|
A:SER39
|
4.9
|
9.4
|
0.7
|
HA
|
A:CYS27
|
4.9
|
7.9
|
1.0
|
CB
|
A:ARG29
|
5.0
|
7.7
|
1.0
|
CA
|
A:ALA26
|
5.0
|
6.3
|
0.9
|
|
Iron binding site 3 out
of 4 in 3tbn
Go back to
Iron Binding Sites List in 3tbn
Iron binding site 3 out
of 4 in the Crystal Structure of A MINER2 Homolog: A Type 6 Cdgsh Iron-Sulfur Protein.
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 3 of Crystal Structure of A MINER2 Homolog: A Type 6 Cdgsh Iron-Sulfur Protein. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe81
b:7.6
occ:0.92
|
FE1
|
A:FES81
|
0.0
|
7.6
|
0.9
|
ND1
|
A:HIS76
|
2.1
|
9.2
|
0.9
|
S2
|
A:FES81
|
2.2
|
7.6
|
0.9
|
S1
|
A:FES81
|
2.2
|
7.3
|
0.9
|
SG
|
A:CYS72
|
2.3
|
8.7
|
0.9
|
FE2
|
A:FES81
|
2.7
|
6.5
|
0.9
|
HB3
|
A:HIS76
|
2.9
|
12.6
|
0.9
|
CE1
|
A:HIS76
|
3.0
|
10.3
|
0.9
|
H
|
A:GLY74
|
3.2
|
10.5
|
1.0
|
CG
|
A:HIS76
|
3.2
|
10.0
|
0.9
|
H
|
A:HIS76
|
3.2
|
11.8
|
1.0
|
HE1
|
A:HIS76
|
3.2
|
12.4
|
0.9
|
HA
|
A:CYS72
|
3.2
|
9.7
|
1.0
|
HB2
|
A:CYS72
|
3.3
|
11.0
|
1.0
|
CB
|
A:CYS72
|
3.3
|
9.2
|
1.0
|
CB
|
A:HIS76
|
3.5
|
10.5
|
1.0
|
HD3
|
A:PRO11
|
3.6
|
13.0
|
1.0
|
CA
|
A:CYS72
|
3.7
|
8.1
|
1.0
|
H
|
A:ASP73
|
3.7
|
9.8
|
1.0
|
HA2
|
A:GLY74
|
3.9
|
12.0
|
1.0
|
N
|
A:GLY74
|
3.9
|
8.8
|
1.0
|
N
|
A:HIS76
|
4.0
|
9.8
|
0.9
|
HA
|
A:CYS61
|
4.0
|
7.8
|
1.0
|
HB3
|
A:PRO11
|
4.1
|
14.6
|
0.7
|
NE2
|
A:HIS76
|
4.2
|
11.5
|
0.9
|
HB3
|
A:CYS72
|
4.2
|
11.0
|
1.0
|
N
|
A:ASP73
|
4.2
|
8.1
|
1.0
|
H
|
A:THR75
|
4.2
|
11.2
|
0.7
|
CD2
|
A:HIS76
|
4.2
|
12.1
|
0.9
|
HB2
|
A:HIS76
|
4.3
|
12.6
|
1.0
|
CA
|
A:GLY74
|
4.3
|
10.0
|
1.0
|
C
|
A:CYS72
|
4.4
|
7.5
|
0.9
|
CA
|
A:HIS76
|
4.4
|
10.2
|
1.0
|
CD
|
A:PRO11
|
4.4
|
10.9
|
1.0
|
H
|
A:GLY62
|
4.4
|
7.5
|
1.0
|
N
|
A:THR75
|
4.5
|
9.3
|
0.9
|
SG
|
A:CYS63
|
4.5
|
7.6
|
0.9
|
C
|
A:GLY74
|
4.5
|
9.6
|
1.0
|
N
|
A:PRO11
|
4.6
|
8.5
|
0.9
|
HA
|
A:ALA10
|
4.6
|
11.2
|
0.9
|
HA
|
A:PRO11
|
4.6
|
10.7
|
1.0
|
H
|
A:CYS63
|
4.7
|
7.8
|
0.6
|
HB2
|
A:CYS61
|
4.7
|
8.5
|
1.0
|
SG
|
A:CYS61
|
4.7
|
6.6
|
0.9
|
HB2
|
A:SER66
|
4.8
|
10.6
|
1.0
|
CB
|
A:PRO11
|
4.8
|
12.2
|
1.0
|
CA
|
A:CYS61
|
4.9
|
6.5
|
1.0
|
HG3
|
A:PRO11
|
4.9
|
15.4
|
1.0
|
HB3
|
A:CYS63
|
4.9
|
10.3
|
1.0
|
C
|
A:ALA10
|
4.9
|
8.8
|
0.9
|
HE2
|
A:HIS76
|
4.9
|
13.8
|
0.8
|
HA
|
A:HIS76
|
5.0
|
12.2
|
1.0
|
CA
|
A:PRO11
|
5.0
|
8.9
|
1.0
|
N
|
A:CYS72
|
5.0
|
7.3
|
1.0
|
CB
|
A:CYS61
|
5.0
|
7.1
|
1.0
|
|
Iron binding site 4 out
of 4 in 3tbn
Go back to
Iron Binding Sites List in 3tbn
Iron binding site 4 out
of 4 in the Crystal Structure of A MINER2 Homolog: A Type 6 Cdgsh Iron-Sulfur Protein.
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 4 of Crystal Structure of A MINER2 Homolog: A Type 6 Cdgsh Iron-Sulfur Protein. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe81
b:6.5
occ:0.87
|
FE2
|
A:FES81
|
0.0
|
6.5
|
0.9
|
S2
|
A:FES81
|
2.2
|
7.6
|
0.9
|
S1
|
A:FES81
|
2.2
|
7.3
|
0.9
|
SG
|
A:CYS61
|
2.4
|
6.6
|
0.9
|
SG
|
A:CYS63
|
2.4
|
7.6
|
0.9
|
FE1
|
A:FES81
|
2.7
|
7.6
|
0.9
|
H
|
A:CYS63
|
2.7
|
7.8
|
0.6
|
HB3
|
A:HIS76
|
3.1
|
12.6
|
0.9
|
HA
|
A:CYS61
|
3.4
|
7.8
|
1.0
|
CB
|
A:CYS61
|
3.4
|
7.1
|
1.0
|
CB
|
A:CYS63
|
3.5
|
8.6
|
1.0
|
HB3
|
A:CYS63
|
3.5
|
10.3
|
1.0
|
HB2
|
A:CYS61
|
3.5
|
8.5
|
1.0
|
N
|
A:CYS63
|
3.5
|
6.5
|
0.9
|
H
|
A:GLY62
|
3.5
|
7.5
|
1.0
|
HB2
|
A:SER66
|
3.5
|
10.6
|
1.0
|
H
|
A:LYS64
|
3.6
|
8.2
|
0.7
|
H
|
A:SER66
|
3.7
|
10.2
|
0.8
|
H
|
A:ALA65
|
3.7
|
9.1
|
1.0
|
H
|
A:HIS76
|
3.7
|
11.8
|
1.0
|
HA
|
A:CYS72
|
3.8
|
9.7
|
1.0
|
CA
|
A:CYS61
|
3.8
|
6.5
|
1.0
|
N
|
A:GLY62
|
3.9
|
6.2
|
1.0
|
CA
|
A:CYS63
|
4.0
|
7.7
|
1.0
|
CB
|
A:HIS76
|
4.0
|
10.5
|
1.0
|
N
|
A:LYS64
|
4.1
|
6.8
|
1.0
|
N
|
A:SER66
|
4.2
|
8.5
|
1.0
|
C
|
A:CYS61
|
4.2
|
6.2
|
1.0
|
HB3
|
A:CYS61
|
4.3
|
8.5
|
1.0
|
ND1
|
A:HIS76
|
4.3
|
9.2
|
0.9
|
N
|
A:HIS76
|
4.3
|
9.8
|
0.9
|
HB2
|
A:CYS63
|
4.3
|
10.3
|
0.9
|
HB
|
A:THR75
|
4.3
|
13.9
|
1.0
|
CB
|
A:SER66
|
4.4
|
8.8
|
1.0
|
C
|
A:CYS63
|
4.4
|
6.7
|
0.9
|
N
|
A:ALA65
|
4.5
|
7.6
|
1.0
|
HA
|
A:SER66
|
4.5
|
10.4
|
1.0
|
HB2
|
A:HIS76
|
4.5
|
12.6
|
1.0
|
H
|
A:ASP73
|
4.6
|
9.8
|
1.0
|
HB2
|
A:CYS72
|
4.6
|
11.0
|
1.0
|
CA
|
A:HIS76
|
4.6
|
10.2
|
1.0
|
C
|
A:GLY62
|
4.6
|
6.6
|
1.0
|
CG
|
A:HIS76
|
4.6
|
10.0
|
0.9
|
CA
|
A:SER66
|
4.6
|
8.7
|
1.0
|
HA
|
A:HIS76
|
4.6
|
12.2
|
1.0
|
CA
|
A:CYS72
|
4.7
|
8.1
|
1.0
|
HB3
|
A:SER66
|
4.7
|
10.6
|
1.0
|
SG
|
A:CYS72
|
4.7
|
8.7
|
0.9
|
CA
|
A:GLY62
|
4.8
|
6.7
|
1.0
|
HB3
|
A:ALA65
|
4.9
|
13.3
|
0.9
|
HA
|
A:CYS63
|
4.9
|
9.2
|
1.0
|
CB
|
A:CYS72
|
4.9
|
9.2
|
1.0
|
H
|
A:THR75
|
4.9
|
11.2
|
0.7
|
C
|
A:ALA65
|
5.0
|
8.2
|
0.9
|
|
Reference:
J.Lin,
L.Zhang,
S.Lai,
K.Ye.
Structure and Molecular Evolution of Cdgsh Iron-Sulfur Domains. Plos One V. 6 24790 2011.
ISSN: ESSN 1932-6203
PubMed: 21949752
DOI: 10.1371/JOURNAL.PONE.0024790
Page generated: Sun Aug 4 20:21:12 2024
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