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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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