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Iron in PDB 3myr: Crystal Structure of [Nife] Hydrogenase From Allochromatium Vinosum in Its Ni-A State

Enzymatic activity of Crystal Structure of [Nife] Hydrogenase From Allochromatium Vinosum in Its Ni-A State

All present enzymatic activity of Crystal Structure of [Nife] Hydrogenase From Allochromatium Vinosum in Its Ni-A State:
1.12.99.6;

Protein crystallography data

The structure of Crystal Structure of [Nife] Hydrogenase From Allochromatium Vinosum in Its Ni-A State, PDB code: 3myr was solved by H.Ogata, P.Kellers, W.Lubitz, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 2.10
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 205.750, 216.960, 119.800, 90.00, 90.00, 90.00
R / Rfree (%) 13.8 / 16.8

Other elements in 3myr:

The structure of Crystal Structure of [Nife] Hydrogenase From Allochromatium Vinosum in Its Ni-A State also contains other interesting chemical elements:

Nickel (Ni) 4 atoms
Magnesium (Mg) 4 atoms
Chlorine (Cl) 4 atoms

Iron Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 30; Page 4, Binding sites: 31 - 40; Page 5, Binding sites: 41 - 50; Page 6, Binding sites: 51 - 52;

Binding sites:

The binding sites of Iron atom in the Crystal Structure of [Nife] Hydrogenase From Allochromatium Vinosum in Its Ni-A State (pdb code 3myr). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 52 binding sites of Iron where determined in the Crystal Structure of [Nife] Hydrogenase From Allochromatium Vinosum in Its Ni-A State, PDB code: 3myr:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 52 in 3myr

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Iron binding site 1 out of 52 in the Crystal Structure of [Nife] Hydrogenase From Allochromatium Vinosum in Its Ni-A State


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 [Nife] Hydrogenase From Allochromatium Vinosum in Its Ni-A State within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe2001

b:15.8
occ:1.00
FE1 A:SF42001 0.0 15.8 1.0
S3 A:SF42001 2.2 16.7 1.0
S4 A:SF42001 2.3 21.0 1.0
SG A:CYS149 2.3 16.5 1.0
S2 A:SF42001 2.3 18.2 1.0
FE4 A:SF42001 2.7 19.5 1.0
FE3 A:SF42001 2.8 21.7 1.0
FE2 A:SF42001 2.8 17.1 0.5
CA A:CYS149 3.4 14.6 1.0
CB A:CYS149 3.4 15.3 1.0
C A:CYS149 3.9 15.1 1.0
O A:HOH3128 4.0 11.6 1.0
S1 A:SF42001 4.0 18.2 0.5
CG B:ARG1059 4.0 16.5 1.0
N A:PRO150 4.4 16.0 1.0
SG A:CYS115 4.5 18.7 1.0
FE2 A:SF42001 4.5 22.7 0.5
O A:CYS149 4.5 17.7 1.0
SG A:CYS16 4.5 20.9 1.0
O A:GLY148 4.6 16.1 1.0
S1 A:SF42001 4.6 19.2 0.5
CA A:PRO150 4.6 15.1 1.0
ND1 B:HIS1214 4.7 17.3 1.0
CE1 B:HIS1214 4.7 14.5 1.0
N A:CYS149 4.7 17.2 1.0
NE B:ARG1059 4.7 16.5 1.0
SG A:CYS19 4.9 21.7 1.0

Iron binding site 2 out of 52 in 3myr

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Iron binding site 2 out of 52 in the Crystal Structure of [Nife] Hydrogenase From Allochromatium Vinosum in Its Ni-A State


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 [Nife] Hydrogenase From Allochromatium Vinosum in Its Ni-A State within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe2001

b:17.1
occ:0.50
FE2 A:SF42001 0.0 17.1 0.5
FE2 A:SF42001 1.9 22.7 0.5
SG A:CYS19 2.3 21.7 1.0
S3 A:SF42001 2.3 16.7 1.0
S4 A:SF42001 2.3 21.0 1.0
S1 A:SF42001 2.4 18.2 0.5
FE4 A:SF42001 2.6 19.5 1.0
FE1 A:SF42001 2.8 15.8 1.0
S1 A:SF42001 2.8 19.2 0.5
FE3 A:SF42001 2.8 21.7 1.0
S2 A:SF42001 3.8 18.2 1.0
CB A:CYS19 3.8 21.0 1.0
N A:CYS19 3.9 18.5 1.0
O A:HOH3198 4.2 15.7 1.0
CA A:GLY113 4.2 14.0 1.0
OD1 A:ASP75 4.3 37.0 1.0
CA A:PRO150 4.3 15.1 1.0
CA A:CYS19 4.4 19.0 1.0
CB A:PRO150 4.4 15.7 1.0
O A:GLY148 4.6 16.1 1.0
C A:GLY18 4.6 20.5 1.0
CA A:CYS149 4.7 14.6 1.0
SG A:CYS16 4.7 20.9 1.0
CA A:GLY18 4.9 18.0 1.0
N A:PRO150 4.9 16.0 1.0
SG A:CYS149 4.9 16.5 1.0

Iron binding site 3 out of 52 in 3myr

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Iron binding site 3 out of 52 in the Crystal Structure of [Nife] Hydrogenase From Allochromatium Vinosum in Its Ni-A State


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 [Nife] Hydrogenase From Allochromatium Vinosum in Its Ni-A State within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe2001

b:22.7
occ:0.50
FE2 A:SF42001 0.0 22.7 0.5
S1 A:SF42001 1.7 18.2 0.5
FE2 A:SF42001 1.9 17.1 0.5
S1 A:SF42001 2.2 19.2 0.5
SG A:CYS19 2.3 21.7 1.0
OD1 A:ASP75 2.4 37.0 1.0
O A:HOH3198 3.2 15.7 1.0
CB A:CYS19 3.2 21.0 1.0
FE3 A:SF42001 3.3 21.7 1.0
CG A:ASP75 3.4 31.6 1.0
FE4 A:SF42001 3.4 19.5 1.0
S4 A:SF42001 3.7 21.0 1.0
OD2 A:ASP75 3.8 41.6 1.0
N A:CYS19 3.9 18.5 1.0
S3 A:SF42001 4.0 16.7 1.0
CA A:CYS19 4.1 19.0 1.0
CB A:GLU15 4.2 19.1 1.0
N A:GLY76 4.2 18.0 1.0
O A:VAL112 4.2 16.2 1.0
CA A:GLY113 4.5 14.0 1.0
FE1 A:SF42001 4.5 15.8 1.0
CB A:ASP75 4.6 23.5 1.0
CA A:ASP75 4.7 21.1 1.0
S2 A:SF42001 4.7 18.2 1.0
C A:ASP75 4.8 21.1 1.0
N A:CYS16 4.8 18.1 1.0
CA A:GLU15 4.9 20.4 1.0
C A:GLY18 5.0 20.5 1.0
CA A:GLY76 5.0 15.9 1.0

Iron binding site 4 out of 52 in 3myr

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Iron binding site 4 out of 52 in the Crystal Structure of [Nife] Hydrogenase From Allochromatium Vinosum in Its Ni-A State


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 [Nife] Hydrogenase From Allochromatium Vinosum in Its Ni-A State within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe2001

b:21.7
occ:1.00
FE3 A:SF42001 0.0 21.7 1.0
SG A:CYS115 2.2 18.7 1.0
S2 A:SF42001 2.3 18.2 1.0
S4 A:SF42001 2.3 21.0 1.0
S1 A:SF42001 2.4 18.2 0.5
FE1 A:SF42001 2.8 15.8 1.0
FE2 A:SF42001 2.8 17.1 0.5
FE4 A:SF42001 3.0 19.5 1.0
CB A:CYS115 3.2 14.7 1.0
FE2 A:SF42001 3.3 22.7 0.5
N A:CYS115 3.9 17.3 1.0
S1 A:SF42001 3.9 19.2 0.5
O A:HOH3198 3.9 15.7 1.0
O A:HOH3097 4.0 13.1 1.0
S3 A:SF42001 4.0 16.7 1.0
O A:HOH3128 4.0 11.6 1.0
CA A:CYS115 4.2 17.6 1.0
SG A:CYS149 4.6 16.5 1.0
SG A:CYS19 4.8 21.7 1.0
N A:THR114 5.0 15.8 1.0

Iron binding site 5 out of 52 in 3myr

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Iron binding site 5 out of 52 in the Crystal Structure of [Nife] Hydrogenase From Allochromatium Vinosum in Its Ni-A State


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Crystal Structure of [Nife] Hydrogenase From Allochromatium Vinosum in Its Ni-A State within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe2001

b:19.5
occ:1.00
FE4 A:SF42001 0.0 19.5 1.0
S2 A:SF42001 2.2 18.2 1.0
S3 A:SF42001 2.3 16.7 1.0
S1 A:SF42001 2.3 19.2 0.5
SG A:CYS16 2.3 20.9 1.0
S1 A:SF42001 2.4 18.2 0.5
FE2 A:SF42001 2.6 17.1 0.5
FE1 A:SF42001 2.7 15.8 1.0
FE3 A:SF42001 3.0 21.7 1.0
CB A:CYS16 3.4 17.1 1.0
FE2 A:SF42001 3.4 22.7 0.5
N A:CYS16 3.7 18.1 1.0
S4 A:SF42001 3.9 21.0 1.0
CA A:CYS16 4.0 19.5 1.0
N A:GLY18 4.1 20.8 1.0
CE1 B:HIS1214 4.3 14.5 1.0
CA A:GLY18 4.3 18.0 1.0
N A:THR17 4.4 20.7 1.0
C A:CYS16 4.5 19.5 1.0
SG A:CYS19 4.7 21.7 1.0
N A:CYS19 4.7 18.5 1.0
O A:HOH3097 4.7 13.1 1.0
SG A:CYS149 4.8 16.5 1.0
CG B:ARG1059 4.8 16.5 1.0
C A:GLU15 4.8 21.6 1.0
ND1 B:HIS1214 4.9 17.3 1.0
C A:GLY18 4.9 20.5 1.0
SG A:CYS115 5.0 18.7 1.0

Iron binding site 6 out of 52 in 3myr

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Iron binding site 6 out of 52 in the Crystal Structure of [Nife] Hydrogenase From Allochromatium Vinosum in Its Ni-A State


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Crystal Structure of [Nife] Hydrogenase From Allochromatium Vinosum in Its Ni-A State within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe2002

b:14.7
occ:1.00
FE1 A:SF42002 0.0 14.7 1.0
S3 A:SF42002 2.3 13.2 1.0
S4 A:SF42002 2.3 13.9 1.0
SG A:CYS190 2.3 17.0 1.0
S2 A:SF42002 2.3 12.4 1.0
FE3 A:SF42002 2.7 14.2 1.0
FE4 A:SF42002 2.7 13.9 1.0
FE2 A:SF42002 2.8 13.2 1.0
CB A:CYS190 3.1 15.6 1.0
S1 A:SF42002 3.9 13.6 1.0
CB A:ARG192 4.0 13.9 1.0
CG1 A:VAL243 4.4 11.4 1.0
N A:ARG193 4.5 16.6 1.0
ND1 A:HIS187 4.5 16.1 1.0
CA A:CYS190 4.6 16.3 1.0
C A:ARG192 4.6 16.5 1.0
CA A:ARG192 4.6 16.4 1.0
N A:ARG192 4.6 14.9 1.0
CG A:ARG192 4.7 16.2 1.0
SG A:CYS221 4.8 17.7 1.0
SG A:CYS215 4.9 18.8 1.0
CG2 A:VAL243 5.0 14.3 1.0
C A:CYS190 5.0 18.3 1.0
CA A:ARG193 5.0 15.2 1.0

Iron binding site 7 out of 52 in 3myr

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Iron binding site 7 out of 52 in the Crystal Structure of [Nife] Hydrogenase From Allochromatium Vinosum in Its Ni-A State


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Crystal Structure of [Nife] Hydrogenase From Allochromatium Vinosum in Its Ni-A State within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe2002

b:13.2
occ:1.00
FE2 A:SF42002 0.0 13.2 1.0
SG A:CYS215 2.2 18.8 1.0
S1 A:SF42002 2.3 13.6 1.0
S4 A:SF42002 2.3 13.9 1.0
S3 A:SF42002 2.3 13.2 1.0
FE4 A:SF42002 2.7 13.9 1.0
FE3 A:SF42002 2.7 14.2 1.0
FE1 A:SF42002 2.8 14.7 1.0
CB A:CYS215 3.4 15.0 1.0
N A:LEU216 3.8 18.3 1.0
CA A:CYS215 3.9 18.0 1.0
S2 A:SF42002 3.9 12.4 1.0
N A:TYR217 4.1 17.4 1.0
C A:CYS215 4.3 18.2 1.0
CB A:TYR196 4.3 17.6 1.0
ND1 A:HIS187 4.4 16.1 1.0
CD1 A:TYR196 4.4 18.8 1.0
CB A:TYR217 4.5 16.3 1.0
CB A:ARG192 4.5 13.9 1.0
CA A:TYR217 4.7 19.5 1.0
CA A:LEU216 4.7 15.8 1.0
CE1 A:HIS187 4.7 19.3 1.0
C A:LEU216 4.8 17.9 1.0
CG A:TYR196 4.8 18.9 1.0
SG A:CYS221 4.8 17.7 1.0
O A:ARG192 4.8 16.9 1.0
SG A:CYS190 4.9 17.0 1.0
C A:ARG192 5.0 16.5 1.0

Iron binding site 8 out of 52 in 3myr

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Iron binding site 8 out of 52 in the Crystal Structure of [Nife] Hydrogenase From Allochromatium Vinosum in Its Ni-A State


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Crystal Structure of [Nife] Hydrogenase From Allochromatium Vinosum in Its Ni-A State within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe2002

b:14.2
occ:1.00
FE3 A:SF42002 0.0 14.2 1.0
S1 A:SF42002 2.2 13.6 1.0
SG A:CYS221 2.3 17.7 1.0
S2 A:SF42002 2.3 12.4 1.0
S4 A:SF42002 2.3 13.9 1.0
FE1 A:SF42002 2.7 14.7 1.0
FE4 A:SF42002 2.7 13.9 1.0
FE2 A:SF42002 2.7 13.2 1.0
CB A:CYS221 3.2 17.1 1.0
S3 A:SF42002 3.9 13.2 1.0
N A:GLY223 4.5 17.4 1.0
CA A:GLY223 4.5 17.2 1.0
CD A:PRO224 4.6 17.6 1.0
ND1 A:HIS187 4.6 16.1 1.0
CG2 A:VAL243 4.6 14.3 1.0
CA A:CYS221 4.6 18.7 1.0
SG A:CYS215 4.7 18.8 1.0
SG A:CYS190 4.8 17.0 1.0
N A:TYR217 4.8 17.4 1.0
C A:CYS221 4.9 19.1 1.0
N A:LEU216 4.9 18.3 1.0
CB A:LEU216 4.9 16.0 1.0

Iron binding site 9 out of 52 in 3myr

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Iron binding site 9 out of 52 in the Crystal Structure of [Nife] Hydrogenase From Allochromatium Vinosum in Its Ni-A State


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 9 of Crystal Structure of [Nife] Hydrogenase From Allochromatium Vinosum in Its Ni-A State within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe2002

b:13.9
occ:1.00
FE4 A:SF42002 0.0 13.9 1.0
ND1 A:HIS187 2.0 16.1 1.0
S2 A:SF42002 2.3 12.4 1.0
S1 A:SF42002 2.3 13.6 1.0
S3 A:SF42002 2.3 13.2 1.0
FE2 A:SF42002 2.7 13.2 1.0
FE3 A:SF42002 2.7 14.2 1.0
FE1 A:SF42002 2.7 14.7 1.0
CE1 A:HIS187 2.9 19.3 1.0
CG A:HIS187 3.1 14.4 1.0
CB A:HIS187 3.6 14.3 1.0
S4 A:SF42002 3.9 13.9 1.0
CA A:HIS187 3.9 15.7 1.0
NE2 A:HIS187 4.1 18.2 1.0
CD A:PRO224 4.2 17.6 1.0
CD2 A:HIS187 4.2 15.2 1.0
CG A:PRO224 4.4 16.1 1.0
SG A:CYS215 4.6 18.8 1.0
CB A:CYS190 4.6 15.6 1.0
SG A:CYS190 4.7 17.0 1.0
SG A:CYS221 4.7 17.7 1.0
O A:HIS187 4.8 17.2 1.0
N A:PRO224 4.8 18.3 1.0
CD A:ARG193 4.9 13.0 1.0
C A:HIS187 4.9 18.0 1.0
N A:HIS187 4.9 15.0 1.0
CD1 A:TYR196 4.9 18.8 1.0
CA A:GLY223 5.0 17.2 1.0

Iron binding site 10 out of 52 in 3myr

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Iron binding site 10 out of 52 in the Crystal Structure of [Nife] Hydrogenase From Allochromatium Vinosum in Its Ni-A State


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 10 of Crystal Structure of [Nife] Hydrogenase From Allochromatium Vinosum in Its Ni-A State within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe2003

b:14.4
occ:1.00
FE1 A:F3S2003 0.0 14.4 1.0
S2 A:F3S2003 2.2 12.7 1.0
S3 A:F3S2003 2.3 14.3 1.0
S1 A:F3S2003 2.3 16.4 1.0
SG A:CYS249 2.3 16.8 1.0
FE3 A:F3S2003 2.7 14.5 1.0
FE4 A:F3S2003 2.7 13.8 1.0
CB A:CYS249 3.3 15.0 1.0
CA A:CYS249 3.6 15.1 1.0
S4 A:F3S2003 3.9 12.8 1.0
N A:LEU250 4.0 16.1 1.0
N A:GLY251 4.2 16.9 1.0
C A:CYS249 4.2 17.0 1.0
N A:CYS252 4.4 17.5 1.0
CG2 A:THR226 4.5 11.4 1.0
CG1 A:ILE186 4.7 18.2 1.0
SG A:CYS252 4.8 17.2 1.0
CA A:GLY251 4.8 17.6 1.0
SG A:CYS230 4.9 15.9 1.0
CD1 A:ILE186 4.9 13.3 1.0
O B:HOH3546 4.9 21.4 1.0
N A:CYS249 5.0 17.5 1.0

Reference:

H.Ogata, P.Kellers, W.Lubitz. The Crystal Structure of the [Nife] Hydrogenase From the Photosynthetic Bacterium Allochromatium Vinosum: Characterization of the Oxidized Enzyme (Ni-A State). J.Mol.Biol. V. 402 428 2010.
ISSN: ISSN 0022-2836
PubMed: 20673834
DOI: 10.1016/J.JMB.2010.07.041
Page generated: Sun Dec 13 15:13:09 2020

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