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Nickel in PDB 2x27: Crystal Structure of the Outer Membrane Protein Oprg From Pseudomonas Aeruginosa

Protein crystallography data

The structure of Crystal Structure of the Outer Membrane Protein Oprg From Pseudomonas Aeruginosa, PDB code: 2x27 was solved by D.S.Touw, D.R.Patel, B.Van Den Berg, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 14.99 / 2.40
Space group I 2 2 2
Cell size a, b, c (Å), α, β, γ (°) 52.050, 58.380, 164.433, 90.00, 90.00, 90.00
R / Rfree (%) 19.1 / 26.9

Nickel Binding Sites:

The binding sites of Nickel atom in the Crystal Structure of the Outer Membrane Protein Oprg From Pseudomonas Aeruginosa (pdb code 2x27). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 3 binding sites of Nickel where determined in the Crystal Structure of the Outer Membrane Protein Oprg From Pseudomonas Aeruginosa, PDB code: 2x27:
Jump to Nickel binding site number: 1; 2; 3;

Nickel binding site 1 out of 3 in 2x27

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Nickel binding site 1 out of 3 in the Crystal Structure of the Outer Membrane Protein Oprg From Pseudomonas Aeruginosa


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of Crystal Structure of the Outer Membrane Protein Oprg From Pseudomonas Aeruginosa within 5.0Å range:
probe atom residue distance (Å) B Occ
X:Ni1213

b:32.7
occ:1.00
OD1 X:ASP173 2.3 21.8 1.0
OD2 X:ASP175 2.4 22.2 1.0
OD1 X:ASP198 2.5 22.1 1.0
O X:HOH2099 2.6 29.0 1.0
OD2 X:ASP198 2.7 23.6 1.0
OD1 X:ASP175 2.8 22.9 1.0
CG X:ASP198 2.9 21.4 1.0
CG X:ASP175 2.9 23.0 1.0
CG X:ASP173 3.5 21.9 1.0
N X:ILE174 4.2 17.8 1.0
OD2 X:ASP196 4.2 33.6 1.0
CG X:ASP196 4.2 27.9 1.0
O X:HOH2091 4.2 19.3 1.0
OD2 X:ASP173 4.3 24.6 1.0
CA X:ASP173 4.3 17.4 1.0
CB X:ASP196 4.3 26.1 1.0
CB X:ASP198 4.4 22.4 1.0
O X:ILE174 4.4 18.3 1.0
CB X:ASP173 4.4 19.3 1.0
CB X:ASP175 4.4 12.8 1.0
C X:ASP173 4.5 18.1 1.0
C X:ILE174 4.5 19.3 1.0
O X:HOH2055 4.6 35.8 1.0
OD1 X:ASP196 4.7 25.4 1.0
OH X:TYR171 4.7 22.6 1.0
N X:ASP175 4.8 20.5 1.0
O X:HOH2083 4.9 21.7 1.0
O X:HOH2100 4.9 32.1 1.0
CA X:ASP196 4.9 22.4 1.0

Nickel binding site 2 out of 3 in 2x27

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Nickel binding site 2 out of 3 in the Crystal Structure of the Outer Membrane Protein Oprg From Pseudomonas Aeruginosa


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of Crystal Structure of the Outer Membrane Protein Oprg From Pseudomonas Aeruginosa within 5.0Å range:
probe atom residue distance (Å) B Occ
X:Ni1214

b:28.2
occ:1.00
NE2 X:HIS162 2.2 23.0 1.0
O X:HOH2103 2.3 26.1 1.0
ND1 X:HIS211 2.4 22.0 1.0
O X:HOH2087 2.6 33.2 1.0
O X:HOH2105 3.1 23.7 1.0
CD2 X:HIS162 3.2 20.6 1.0
CE1 X:HIS162 3.3 22.8 1.0
CE1 X:HIS211 3.3 24.7 1.0
CG X:HIS211 3.4 21.1 1.0
CB X:HIS211 3.6 22.4 1.0
O X:HOH2102 4.2 27.3 1.0
N X:HIS211 4.3 20.5 1.0
CG X:HIS162 4.3 22.8 1.0
ND1 X:HIS162 4.4 25.1 1.0
NE2 X:HIS211 4.4 24.1 1.0
CD2 X:HIS211 4.5 21.9 1.0
CA X:HIS211 4.6 23.4 1.0

Nickel binding site 3 out of 3 in 2x27

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Nickel binding site 3 out of 3 in the Crystal Structure of the Outer Membrane Protein Oprg From Pseudomonas Aeruginosa


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 3 of Crystal Structure of the Outer Membrane Protein Oprg From Pseudomonas Aeruginosa within 5.0Å range:
probe atom residue distance (Å) B Occ
X:Ni1215

b:31.6
occ:1.00
OD1 X:ASP23 2.3 25.1 1.0
CG X:ASP23 3.2 26.4 1.0
OD2 X:ASP23 3.3 26.2 1.0
O X:PRO21 4.0 26.3 1.0
O X:VAL42 4.1 23.8 1.0
N X:ASP23 4.5 21.0 1.0
CB X:ASP23 4.6 22.0 1.0
O X:HOH2022 4.6 39.7 1.0
O X:ASP23 4.8 24.3 1.0
C X:PRO21 4.9 25.0 1.0

Reference:

D.S.Touw, D.R.Patel, B.Van Den Berg. The Crystal Structure of Oprg From Pseudomonas Aeruginosa, A Potential Channel For Transport of Hydrophobic Molecules Across the Outer Membrane. Plos One V. 5 15016 2010.
ISSN: ESSN 1932-6203
PubMed: 21124774
DOI: 10.1371/JOURNAL.PONE.0015016
Page generated: Fri Sep 25 08:16:38 2020
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