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Nickel in PDB 2rab: Structure of Glutathione Amide Reductase From Chromatium Gracile in Complex with Nad

Protein crystallography data

The structure of Structure of Glutathione Amide Reductase From Chromatium Gracile in Complex with Nad, PDB code: 2rab was solved by F.Van Petegem, D.De Vos, S.Savvides, B.Vergauwen, J.Van Beeumen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 15.00 / 2.50
Space group P 41
Cell size a, b, c (Å), α, β, γ (°) 71.989, 71.989, 224.603, 90.00, 90.00, 90.00
R / Rfree (%) 18.5 / 23.3

Nickel Binding Sites:

The binding sites of Nickel atom in the Structure of Glutathione Amide Reductase From Chromatium Gracile in Complex with Nad (pdb code 2rab). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 4 binding sites of Nickel where determined in the Structure of Glutathione Amide Reductase From Chromatium Gracile in Complex with Nad, PDB code: 2rab:
Jump to Nickel binding site number: 1; 2; 3; 4;

Nickel binding site 1 out of 4 in 2rab

Go back to Nickel Binding Sites List in 2rab
Nickel binding site 1 out of 4 in the Structure of Glutathione Amide Reductase From Chromatium Gracile in Complex with Nad


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of Structure of Glutathione Amide Reductase From Chromatium Gracile in Complex with Nad within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni466

b:42.9
occ:1.00
O A:HOH812 1.9 23.4 1.0
NE2 A:HIS120 2.1 31.8 1.0
O A:HOH858 2.2 33.6 1.0
O A:HOH857 2.6 44.0 1.0
O A:HOH859 2.9 40.6 1.0
CE1 A:HIS120 3.1 32.2 1.0
CD2 A:HIS120 3.2 31.4 1.0
OD2 A:ASP118 3.9 31.9 1.0
ND1 A:HIS120 4.2 31.2 1.0
CG A:HIS120 4.3 30.8 1.0
OG1 A:THR121 4.3 30.2 1.0
CG A:ASP118 4.7 31.2 1.0
OD1 A:ASP118 4.8 31.8 1.0

Nickel binding site 2 out of 4 in 2rab

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Nickel binding site 2 out of 4 in the Structure of Glutathione Amide Reductase From Chromatium Gracile in Complex with Nad


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of Structure of Glutathione Amide Reductase From Chromatium Gracile in Complex with Nad within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni468

b:42.7
occ:1.00
ND1 A:HIS4 1.9 35.0 1.0
N A:GLN3 2.0 37.5 1.0
N A:HIS4 2.1 35.6 1.0
N A:THR2 2.1 37.6 1.0
C A:THR2 2.9 37.7 1.0
CG A:HIS4 2.9 34.9 1.0
CE1 A:HIS4 2.9 35.2 1.0
C A:GLN3 3.0 36.5 1.0
CA A:THR2 3.0 37.8 1.0
CA A:GLN3 3.0 36.9 1.0
CA A:HIS4 3.1 34.8 1.0
CB A:HIS4 3.2 34.7 1.0
N A:PHE5 3.7 33.6 1.0
C A:HIS4 3.8 34.3 1.0
CB A:THR2 3.9 37.9 1.0
CD2 A:PHE5 3.9 32.1 1.0
NE2 A:HIS4 4.0 35.7 1.0
CD2 A:HIS4 4.0 34.9 1.0
O A:THR2 4.0 37.8 1.0
CB A:GLN3 4.0 37.2 1.0
O A:GLN3 4.1 36.7 1.0
CE2 A:PHE5 4.2 32.1 1.0
CG A:PHE5 4.7 32.9 1.0
O A:HIS4 4.8 34.3 1.0
CG2 A:THR2 4.8 38.7 1.0
O A:SER130 4.9 29.8 1.0
CA A:PHE5 4.9 32.9 1.0
OG1 A:THR2 5.0 38.4 1.0

Nickel binding site 3 out of 4 in 2rab

Go back to Nickel Binding Sites List in 2rab
Nickel binding site 3 out of 4 in the Structure of Glutathione Amide Reductase From Chromatium Gracile in Complex with Nad


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 3 of Structure of Glutathione Amide Reductase From Chromatium Gracile in Complex with Nad within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ni466

b:46.9
occ:1.00
O B:HOH800 2.0 23.4 1.0
NE2 B:HIS120 2.2 33.3 1.0
O B:HOH802 2.3 31.8 1.0
O B:HOH801 3.0 43.8 1.0
CE1 B:HIS120 3.2 34.1 1.0
CD2 B:HIS120 3.2 32.9 1.0
OD2 B:ASP118 4.0 34.4 1.0
ND1 B:HIS120 4.3 33.1 1.0
CG2 B:THR121 4.3 33.5 1.0
CG B:HIS120 4.4 32.7 1.0
CG B:ASP118 4.8 33.6 1.0
OD1 B:ASP118 4.8 34.1 1.0

Nickel binding site 4 out of 4 in 2rab

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Nickel binding site 4 out of 4 in the Structure of Glutathione Amide Reductase From Chromatium Gracile in Complex with Nad


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 4 of Structure of Glutathione Amide Reductase From Chromatium Gracile in Complex with Nad within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ni468

b:42.2
occ:1.00
ND1 B:HIS4 1.9 32.8 1.0
N B:GLN3 1.9 35.3 1.0
N B:THR2 2.0 35.5 1.0
N B:HIS4 2.0 34.3 1.0
C B:THR2 2.8 35.4 1.0
CG B:HIS4 2.8 33.5 1.0
C B:GLN3 2.9 34.8 1.0
CA B:THR2 2.9 35.6 1.0
CE1 B:HIS4 2.9 32.4 1.0
CA B:GLN3 2.9 34.9 1.0
CA B:HIS4 3.0 33.8 1.0
CB B:HIS4 3.2 33.8 1.0
N B:PHE5 3.7 33.2 1.0
C B:HIS4 3.7 33.5 1.0
CB B:GLN3 3.8 35.0 1.0
CB B:THR2 3.9 35.6 1.0
CD2 B:HIS4 4.0 33.8 1.0
NE2 B:HIS4 4.0 33.4 1.0
O B:THR2 4.0 35.5 1.0
CD2 B:PHE5 4.0 34.1 1.0
CG2 B:THR2 4.1 35.9 1.0
O B:GLN3 4.1 35.0 1.0
CE2 B:PHE5 4.3 33.9 1.0
O B:HIS4 4.8 33.6 1.0
CG B:PHE5 4.8 33.6 1.0
O B:SER130 4.8 33.4 1.0
CA B:PHE5 4.9 32.8 1.0

Reference:

F.Van Petegem, D.De Vos, S.Savvides, B.Vergauwen, J.Van Beeumen. Understanding Nicotinamide Dinucleotide Cofactor and Substrate Specificity in Class I Flavoprotein Disulfide Oxidoreductases: Crystallographic Analysis of A Glutathione Amide Reductase. J.Mol.Biol. V. 374 883 2007.
ISSN: ISSN 0022-2836
PubMed: 17977556
DOI: 10.1016/J.JMB.2007.09.072
Page generated: Fri Sep 25 08:14:05 2020
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