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Nickel in PDB 3dp8: Structural Characterization of A Putative Endogenous Metal Chelator in the Periplasmic Nickel Transporter Nika (Nickel Butane-1,2,4- Tricarboxylate Form)

Protein crystallography data

The structure of Structural Characterization of A Putative Endogenous Metal Chelator in the Periplasmic Nickel Transporter Nika (Nickel Butane-1,2,4- Tricarboxylate Form), PDB code: 3dp8 was solved by M.V.Cherrier, C.Cavazza, C.Bochot, D.Lemaire, J.C.Fontecilla-Camps, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 2.50
Space group P 62
Cell size a, b, c (Å), α, β, γ (°) 158.570, 158.570, 134.940, 90.00, 90.00, 120.00
R / Rfree (%) 19.9 / 27

Nickel Binding Sites:

The binding sites of Nickel atom in the Structural Characterization of A Putative Endogenous Metal Chelator in the Periplasmic Nickel Transporter Nika (Nickel Butane-1,2,4- Tricarboxylate Form) (pdb code 3dp8). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 3 binding sites of Nickel where determined in the Structural Characterization of A Putative Endogenous Metal Chelator in the Periplasmic Nickel Transporter Nika (Nickel Butane-1,2,4- Tricarboxylate Form), PDB code: 3dp8:
Jump to Nickel binding site number: 1; 2; 3;

Nickel binding site 1 out of 3 in 3dp8

Go back to Nickel Binding Sites List in 3dp8
Nickel binding site 1 out of 3 in the Structural Characterization of A Putative Endogenous Metal Chelator in the Periplasmic Nickel Transporter Nika (Nickel Butane-1,2,4- Tricarboxylate Form)


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of Structural Characterization of A Putative Endogenous Metal Chelator in the Periplasmic Nickel Transporter Nika (Nickel Butane-1,2,4- Tricarboxylate Form) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni503

b:78.8
occ:1.00
C5 A:HCT511 2.0 56.5 1.0
O6 A:HCT511 2.1 49.3 1.0
C2 A:HCT511 2.5 53.9 1.0
C3 A:HCT511 2.8 52.6 1.0
C7 A:HCT511 2.9 47.5 1.0
O1 A:HCT511 2.9 61.1 1.0
C4 A:HCT511 3.0 55.5 1.0
C6 A:HCT511 3.1 55.2 1.0
C1 A:HCT511 3.1 61.3 1.0
O3 A:HCT511 3.3 50.3 1.0
O5 A:HCT511 4.1 33.3 1.0
O4 A:HCT511 4.2 57.7 1.0
NH2 A:ARG137 4.3 38.4 1.0
O2 A:HCT511 4.3 60.6 1.0
NE1 A:TRP398 4.4 38.5 1.0
CL A:CL510 4.4 90.1 1.0
CZ2 A:TRP398 4.5 36.8 1.0
CE2 A:TRP398 4.5 38.4 1.0

Nickel binding site 2 out of 3 in 3dp8

Go back to Nickel Binding Sites List in 3dp8
Nickel binding site 2 out of 3 in the Structural Characterization of A Putative Endogenous Metal Chelator in the Periplasmic Nickel Transporter Nika (Nickel Butane-1,2,4- Tricarboxylate Form)


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of Structural Characterization of A Putative Endogenous Metal Chelator in the Periplasmic Nickel Transporter Nika (Nickel Butane-1,2,4- Tricarboxylate Form) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ni503

b:53.5
occ:1.00
O6 B:HCT511 2.0 38.3 1.0
O1 B:HCT511 2.1 49.6 1.0
O3 B:HCT511 2.2 53.0 1.0
NE2 B:HIS416 2.2 45.1 1.0
C2 B:HCT511 2.6 44.0 1.0
C1 B:HCT511 2.6 50.8 1.0
C7 B:HCT511 2.8 41.8 1.0
C3 B:HCT511 2.8 44.2 1.0
CE1 B:HIS416 3.1 48.3 1.0
C4 B:HCT511 3.1 47.1 1.0
C6 B:HCT511 3.2 52.6 1.0
CD2 B:HIS416 3.3 48.5 1.0
C5 B:HCT511 3.6 47.5 1.0
O2 B:HCT511 3.8 50.8 1.0
O5 B:HCT511 4.0 35.7 1.0
ND1 B:HIS416 4.3 49.6 1.0
NH2 B:ARG137 4.3 28.6 1.0
O4 B:HCT511 4.4 52.3 1.0
CG B:HIS416 4.4 48.0 1.0
CZ2 B:TRP398 4.7 37.8 1.0
CD2 B:TYR22 4.9 42.5 1.0
CE2 B:TRP398 5.0 36.1 1.0

Nickel binding site 3 out of 3 in 3dp8

Go back to Nickel Binding Sites List in 3dp8
Nickel binding site 3 out of 3 in the Structural Characterization of A Putative Endogenous Metal Chelator in the Periplasmic Nickel Transporter Nika (Nickel Butane-1,2,4- Tricarboxylate Form)


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 3 of Structural Characterization of A Putative Endogenous Metal Chelator in the Periplasmic Nickel Transporter Nika (Nickel Butane-1,2,4- Tricarboxylate Form) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ni503

b:66.9
occ:1.00
C5 C:HCT509 2.3 64.2 1.0
NE2 C:HIS416 2.4 56.9 1.0
O6 C:HCT509 2.4 50.4 1.0
C2 C:HCT509 2.6 58.4 1.0
O1 C:HCT509 2.6 62.8 1.0
C3 C:HCT509 2.8 56.2 1.0
C7 C:HCT509 2.9 51.0 1.0
C1 C:HCT509 3.0 63.7 1.0
C4 C:HCT509 3.1 58.8 1.0
CE1 C:HIS416 3.3 56.0 1.0
CD2 C:HIS416 3.4 56.7 1.0
C6 C:HCT509 3.5 65.6 1.0
O3 C:HCT509 3.8 65.1 1.0
O5 C:HCT509 4.0 48.2 1.0
O2 C:HCT509 4.3 65.5 1.0
NH2 C:ARG137 4.3 40.8 1.0
ND1 C:HIS416 4.4 57.8 1.0
O4 C:HCT509 4.5 67.9 1.0
CE2 C:TYR382 4.5 55.2 0.3
CG C:HIS416 4.5 56.8 1.0
CZ2 C:TRP398 4.6 48.9 1.0
CE2 C:TRP398 4.9 46.5 1.0
CD2 C:TYR22 4.9 55.1 1.0

Reference:

M.V.Cherrier, C.Cavazza, C.Bochot, D.Lemaire, J.C.Fontecilla-Camps. Structural Characterization of A Putative Endogenous Metal Chelator in the Periplasmic Nickel Transporter Nika Biochemistry V. 47 9937 2008.
ISSN: ISSN 0006-2960
PubMed: 18759453
DOI: 10.1021/BI801051Y
Page generated: Fri Sep 25 08:21:14 2020
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