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Nickel in PDB 4xkr: Crystal Structure of Nika From Staphylococcus Aureus in Complex with Ni-(L-His)(2-Methyl-Thiazolidine Dicarboxylate) (Co-Crystallization with Ni(II) and Cddeltahis Medium Supernatant)

Protein crystallography data

The structure of Crystal Structure of Nika From Staphylococcus Aureus in Complex with Ni-(L-His)(2-Methyl-Thiazolidine Dicarboxylate) (Co-Crystallization with Ni(II) and Cddeltahis Medium Supernatant), PDB code: 4xkr was solved by H.Lebrette, C.Cavazza, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 45.54 / 1.75
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 61.803, 67.373, 115.566, 90.00, 90.00, 90.00
R / Rfree (%) 17.2 / 20.3

Other elements in 4xkr:

The structure of Crystal Structure of Nika From Staphylococcus Aureus in Complex with Ni-(L-His)(2-Methyl-Thiazolidine Dicarboxylate) (Co-Crystallization with Ni(II) and Cddeltahis Medium Supernatant) also contains other interesting chemical elements:

Sodium (Na) 1 atom

Nickel Binding Sites:

The binding sites of Nickel atom in the Crystal Structure of Nika From Staphylococcus Aureus in Complex with Ni-(L-His)(2-Methyl-Thiazolidine Dicarboxylate) (Co-Crystallization with Ni(II) and Cddeltahis Medium Supernatant) (pdb code 4xkr). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total only one binding site of Nickel was determined in the Crystal Structure of Nika From Staphylococcus Aureus in Complex with Ni-(L-His)(2-Methyl-Thiazolidine Dicarboxylate) (Co-Crystallization with Ni(II) and Cddeltahis Medium Supernatant), PDB code: 4xkr:

Nickel binding site 1 out of 1 in 4xkr

Go back to Nickel Binding Sites List in 4xkr
Nickel binding site 1 out of 1 in the Crystal Structure of Nika From Staphylococcus Aureus in Complex with Ni-(L-His)(2-Methyl-Thiazolidine Dicarboxylate) (Co-Crystallization with Ni(II) and Cddeltahis Medium Supernatant)


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 Nika From Staphylococcus Aureus in Complex with Ni-(L-His)(2-Methyl-Thiazolidine Dicarboxylate) (Co-Crystallization with Ni(II) and Cddeltahis Medium Supernatant) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni501

b:12.4
occ:1.00
OAA A:41K503 2.0 11.3 1.0
N A:HIS502 2.1 11.9 1.0
O A:HIS502 2.1 11.4 1.0
ND1 A:HIS502 2.1 13.3 1.0
OXT A:41K503 2.1 15.0 1.0
N A:41K503 2.1 12.2 1.0
C A:HIS502 2.7 13.0 1.0
CA A:HIS502 2.8 12.7 1.0
CA A:41K503 2.8 14.3 1.0
CAE A:41K503 2.8 13.2 1.0
C A:41K503 2.8 15.8 1.0
CAF A:41K503 2.9 12.6 1.0
CE1 A:HIS502 3.1 13.7 1.0
CG A:HIS502 3.1 12.6 1.0
CB A:HIS502 3.4 11.6 1.0
CAB A:41K503 3.8 13.3 1.0
OXT A:HIS502 4.0 13.4 1.0
OAD A:41K503 4.0 12.3 1.0
O A:SER370 4.1 10.9 1.0
O A:41K503 4.1 14.9 1.0
NA A:NA523 4.1 34.1 1.0
NH1 A:ARG234 4.2 13.2 1.0
NE2 A:HIS502 4.2 13.2 1.0
CB A:41K503 4.2 20.4 1.0
NH2 A:ARG234 4.2 13.2 1.0
CD2 A:HIS502 4.2 13.8 1.0
NH2 A:ARG325 4.3 13.9 1.0
SAK A:41K503 4.3 19.8 1.0
CZ A:ARG234 4.6 13.8 1.0
O A:HOH836 4.6 20.6 1.0
CD1 A:LEU17 4.8 15.5 1.0
OH A:TYR369 4.8 15.3 1.0

Reference:

H.Lebrette, E.Borezee-Durant, L.Martin, P.Richaud, E.Boeri Erba, C.Cavazza. Novel Insights Into Nickel Import in Staphylococcus Aureus: Positive Role of Free Histidine and Structural Characterization of A New Thiazolidine-Type Nickel Chelator To Be Published.
Page generated: Wed Dec 16 01:38:16 2020

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