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Magnesium 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
Iron (Fe) 52 atoms
Chlorine (Cl) 4 atoms

Magnesium Binding Sites:

The binding sites of Magnesium 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 Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Crystal Structure of [Nife] Hydrogenase From Allochromatium Vinosum in Its Ni-A State, PDB code: 3myr:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 3myr

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Magnesium binding site 1 out of 4 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 Magnesium with other atoms in the Mg 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
B:Mg2006

b:13.4
occ:1.00
 OE2 B:GLU1042 2.0 20.4 1.0
O B:HOH2007 2.1 14.1 1.0
O B:HOH2008 2.1 15.3 1.0
NE2 B:HIS1561 2.1 20.1 1.0
O B:HOH2009 2.1 12.2 1.0
O B:ALA1506 2.1 19.7 1.0
CD B:GLU1042 3.0 22.7 1.0
CE1 B:HIS1561 3.1 14.8 1.0
CD2 B:HIS1561 3.1 18.3 1.0
C B:ALA1506 3.3 20.1 1.0
OE1 B:GLU1042 3.4 20.0 1.0
N B:ALA1506 3.7 20.0 1.0
CA B:ALA1506 4.0 19.9 1.0
OE1 B:GLU1326 4.1 26.2 1.0
OE1 B:GLN1505 4.2 24.9 1.0
O B:HOH3441 4.2 14.4 1.0
ND1 B:HIS1561 4.2 21.1 1.0
OE2 B:GLU1326 4.2 28.8 1.0
CG B:HIS1561 4.3 22.1 1.0
O B:HOH3669 4.3 15.2 1.0
NZ B:LYS1377 4.4 22.5 1.0
CB B:ALA1506 4.4 18.2 1.0
CG B:GLU1042 4.4 23.6 1.0
N B:VAL1507 4.4 20.4 1.0
CD B:GLU1326 4.6 26.7 1.0
CD B:LYS1377 4.6 21.4 1.0
CA B:VAL1507 4.7 20.6 1.0
C B:GLN1505 4.7 21.5 1.0
CE B:LYS1377 4.8 21.0 1.0

Magnesium binding site 2 out of 4 in 3myr

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Magnesium binding site 2 out of 4 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 Magnesium with other atoms in the Mg 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
D:Mg2006

b:17.1
occ:1.00
 OE2 D:GLU1042 2.0 30.2 1.0
NE2 D:HIS1561 2.1 29.6 1.0
O D:HOH2007 2.1 17.0 1.0
O D:HOH2008 2.1 15.9 1.0
O D:HOH2009 2.1 12.9 1.0
O D:ALA1506 2.2 27.0 1.0
CD D:GLU1042 2.9 33.3 1.0
CE1 D:HIS1561 3.1 30.3 1.0
CD2 D:HIS1561 3.1 24.2 1.0
OE1 D:GLU1042 3.3 31.7 1.0
C D:ALA1506 3.3 27.1 1.0
N D:ALA1506 3.7 27.8 1.0
CA D:ALA1506 4.0 27.9 1.0
OE1 D:GLN1505 4.1 26.6 1.0
OE1 D:GLU1326 4.1 37.9 1.0
ND1 D:HIS1561 4.2 26.0 1.0
OE2 D:GLU1326 4.2 37.9 1.0
CG D:HIS1561 4.2 30.1 1.0
O D:HOH3796 4.3 15.2 1.0
CB D:ALA1506 4.3 23.7 1.0
CG D:GLU1042 4.3 30.6 1.0
NZ D:LYS1377 4.3 34.9 1.0
O D:HOH3788 4.3 13.8 1.0
N D:VAL1507 4.4 28.6 1.0
CD D:GLU1326 4.6 35.0 1.0
CD D:LYS1377 4.7 31.2 1.0
C D:GLN1505 4.7 28.8 1.0
CA D:VAL1507 4.7 28.6 1.0
CA D:GLN1505 4.9 27.7 1.0
CE D:LYS1377 4.9 26.9 1.0

Magnesium binding site 3 out of 4 in 3myr

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Magnesium binding site 3 out of 4 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 Magnesium with other atoms in the Mg 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
F:Mg2006

b:18.0
occ:1.00
 OE2 F:GLU1042 2.0 29.9 1.0
O F:HOH2008 2.0 20.8 1.0
NE2 F:HIS1561 2.1 27.1 1.0
O F:HOH2007 2.1 15.6 1.0
O F:HOH2009 2.1 12.9 1.0
O F:ALA1506 2.1 28.0 1.0
CD F:GLU1042 3.0 29.2 1.0
CD2 F:HIS1561 3.1 25.8 1.0
CE1 F:HIS1561 3.1 25.2 1.0
OE1 F:GLU1042 3.3 30.6 1.0
C F:ALA1506 3.3 28.5 1.0
N F:ALA1506 3.8 28.4 1.0
CA F:ALA1506 4.0 27.6 1.0
OE1 F:GLN1505 4.1 36.1 1.0
OE1 F:GLU1326 4.1 34.9 1.0
O F:HOH3518 4.2 16.0 1.0
NZ F:LYS1377 4.2 30.3 1.0
ND1 F:HIS1561 4.2 27.4 1.0
OE2 F:GLU1326 4.2 32.2 1.0
CG F:HIS1561 4.2 28.0 1.0
CG F:GLU1042 4.3 30.3 1.0
CB F:ALA1506 4.3 24.4 1.0
N F:VAL1507 4.4 27.1 1.0
O F:HOH3038 4.4 13.8 1.0
CD F:GLU1326 4.6 36.8 1.0
CD F:LYS1377 4.6 34.7 1.0
C F:GLN1505 4.7 30.0 1.0
CA F:VAL1507 4.7 27.4 1.0
CE F:LYS1377 4.9 34.0 1.0
CA F:GLN1505 5.0 30.7 1.0

Magnesium binding site 4 out of 4 in 3myr

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Magnesium binding site 4 out of 4 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 Magnesium with other atoms in the Mg 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
H:Mg2006

b:16.0
occ:1.00
 OE2 H:GLU1042 2.0 24.5 1.0
O H:HOH2008 2.1 15.6 1.0
NE2 H:HIS1561 2.1 19.3 1.0
O H:ALA1506 2.2 23.4 1.0
O H:HOH2009 2.2 14.0 1.0
O H:HOH2007 2.2 11.0 1.0
CD H:GLU1042 3.0 22.6 1.0
CE1 H:HIS1561 3.0 16.9 1.0
CD2 H:HIS1561 3.1 20.8 1.0
C H:ALA1506 3.3 23.4 1.0
OE1 H:GLU1042 3.4 20.7 1.0
N H:ALA1506 3.6 23.7 1.0
CA H:ALA1506 4.0 23.0 1.0
OE1 H:GLU1326 4.1 22.6 1.0
OE1 H:GLN1505 4.2 22.3 1.0
ND1 H:HIS1561 4.2 20.3 1.0
NZ H:LYS1377 4.2 25.4 1.0
CG H:HIS1561 4.3 22.3 1.0
OE2 H:GLU1326 4.3 26.4 1.0
CB H:ALA1506 4.3 21.9 1.0
CG H:GLU1042 4.3 20.4 1.0
O H:HOH4076 4.3 16.1 1.0
N H:VAL1507 4.4 22.2 1.0
O H:HOH3523 4.4 15.4 1.0
C H:GLN1505 4.6 23.6 1.0
CD H:GLU1326 4.6 30.6 1.0
CA H:VAL1507 4.6 23.9 1.0
CD H:LYS1377 4.8 25.9 1.0
CE H:LYS1377 4.9 23.7 1.0
CA H:GLN1505 5.0 23.5 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: Wed Aug 14 19:32:21 2024

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