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Nickel in PDB 2cad: Nikr From Helicobacter Pylori in Closed Trans-Conformation and Nickel Bound to 2F, 2X and 2I Sites.

Protein crystallography data

The structure of Nikr From Helicobacter Pylori in Closed Trans-Conformation and Nickel Bound to 2F, 2X and 2I Sites., PDB code: 2cad was solved by C.Dian, K.Schauer, U.Kapp, S.M.Mcsweeney, A.Labigne, L.Terradot, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 61.31 / 2.3
Space group P 61 2 2
Cell size a, b, c (Å), α, β, γ (°) 70.807, 70.807, 228.613, 90.00, 90.00, 120.00
R / Rfree (%) 20.2 / 25.7

Nickel Binding Sites:

The binding sites of Nickel atom in the Nikr From Helicobacter Pylori in Closed Trans-Conformation and Nickel Bound to 2F, 2X and 2I Sites. (pdb code 2cad). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 3 binding sites of Nickel where determined in the Nikr From Helicobacter Pylori in Closed Trans-Conformation and Nickel Bound to 2F, 2X and 2I Sites., PDB code: 2cad:
Jump to Nickel binding site number: 1; 2; 3;

Nickel binding site 1 out of 3 in 2cad

Go back to Nickel Binding Sites List in 2cad
Nickel binding site 1 out of 3 in the Nikr From Helicobacter Pylori in Closed Trans-Conformation and Nickel Bound to 2F, 2X and 2I Sites.


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of Nikr From Helicobacter Pylori in Closed Trans-Conformation and Nickel Bound to 2F, 2X and 2I Sites. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni1152

b:37.1
occ:1.00
O A:HOH2022 2.0 30.7 1.0
NE2 A:HIS74 2.1 39.4 1.0
O A:HOH2062 2.1 24.4 1.0
NE2 A:HIS101 2.4 29.6 1.0
CE1 A:HIS74 3.0 39.6 1.0
CD2 A:HIS74 3.2 36.9 1.0
CE1 A:HIS101 3.3 28.7 1.0
CD2 A:HIS101 3.4 30.0 1.0
O3 A:GOL1151 3.7 49.5 1.0
ND1 A:HIS74 4.1 39.3 1.0
CG A:HIS74 4.3 35.8 1.0
ND1 A:HIS101 4.5 29.5 1.0
CG A:HIS101 4.6 27.4 1.0
C3 A:GOL1151 4.7 48.6 1.0

Nickel binding site 2 out of 3 in 2cad

Go back to Nickel Binding Sites List in 2cad
Nickel binding site 2 out of 3 in the Nikr From Helicobacter Pylori in Closed Trans-Conformation and Nickel Bound to 2F, 2X and 2I Sites.


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of Nikr From Helicobacter Pylori in Closed Trans-Conformation and Nickel Bound to 2F, 2X and 2I Sites. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ni1151

b:25.3
occ:1.00
NE2 B:HIS99 2.0 16.1 1.0
ND1 B:HIS101 2.1 23.3 1.0
SG B:CYS107 2.3 26.8 1.0
CD2 B:HIS99 3.0 17.9 1.0
CE1 B:HIS99 3.0 19.4 1.0
CE1 B:HIS101 3.0 21.1 1.0
CG B:HIS101 3.1 23.1 1.0
CB B:CYS107 3.4 25.5 1.0
CA B:HIS101 3.5 24.8 1.0
CB B:HIS101 3.5 24.0 1.0
CA B:CYS107 4.0 26.1 1.0
O B:ILE100 4.1 22.4 1.0
ND1 B:HIS99 4.1 19.2 1.0
N B:HIS101 4.1 23.6 1.0
CG B:HIS99 4.1 17.6 1.0
NE2 B:HIS101 4.2 19.8 1.0
CD2 B:HIS101 4.2 20.4 1.0
C B:ILE100 4.4 22.0 1.0
N B:CYS107 4.8 28.1 1.0
C B:HIS101 4.8 26.3 1.0
O B:ASN106 4.9 29.4 1.0
CB B:HIS74 4.9 31.6 1.0

Nickel binding site 3 out of 3 in 2cad

Go back to Nickel Binding Sites List in 2cad
Nickel binding site 3 out of 3 in the Nikr From Helicobacter Pylori in Closed Trans-Conformation and Nickel Bound to 2F, 2X and 2I Sites.


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 3 of Nikr From Helicobacter Pylori in Closed Trans-Conformation and Nickel Bound to 2F, 2X and 2I Sites. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ni1152

b:43.4
occ:0.80
O B:GLU104 2.0 37.4 1.0
NE2 B:HIS74 2.1 31.1 1.0
O7 B:CIT1150 2.2 36.0 0.8
O2 B:CIT1150 2.3 32.8 0.8
NE2 B:HIS75 2.3 39.9 1.0
O5 B:CIT1150 2.4 36.4 0.8
CE1 B:HIS74 3.0 30.2 1.0
C6 B:CIT1150 3.0 36.2 0.8
C3 B:CIT1150 3.0 36.8 0.8
CE1 B:HIS75 3.1 40.9 1.0
CD2 B:HIS74 3.1 32.6 1.0
C B:GLU104 3.1 37.4 1.0
CD2 B:HIS75 3.1 39.3 1.0
C1 B:CIT1150 3.3 36.0 0.8
C2 B:CIT1150 3.7 38.0 0.8
CA B:GLU104 3.8 37.6 1.0
ND1 B:HIS75 4.1 39.9 1.0
ND1 B:HIS74 4.1 31.2 1.0
CG B:HIS75 4.2 37.9 1.0
O6 B:CIT1150 4.2 36.8 0.8
CG B:HIS74 4.2 31.4 1.0
O3 B:CIT1150 4.2 36.0 0.8
N B:HIS105 4.2 37.8 1.0
O3 B:GOL1148 4.3 40.8 1.0
CB B:GLU104 4.3 38.6 1.0
C4 B:CIT1150 4.3 37.2 0.8
O1 B:CIT1150 4.4 35.9 0.8
CA B:HIS105 4.5 37.7 1.0
C5 B:CIT1150 4.7 37.4 0.8
C3 B:GOL1148 4.9 44.2 1.0
O B:ASP103 4.9 35.8 1.0

Reference:

C.Dian, K.Schauer, U.Kapp, S.M.Mcsweeney, A.Labigne, L.Terradot. Structural Basis of the Nickel Response in Helicobacter Pylori: Crystal Structures of Hpnikr in Apo and Nickel-Bound States. J.Mol.Biol. V. 361 715 2006.
ISSN: ISSN 0022-2836
PubMed: 16872629
DOI: 10.1016/J.JMB.2006.06.058
Page generated: Fri Sep 25 08:07:32 2020
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