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Nickel in PDB 1sk3: Crystal Structure of the C-Terminal Peptidoglycan-Binding Domain of Human Peptidoglycan Recognition Protein Ialpha

Protein crystallography data

The structure of Crystal Structure of the C-Terminal Peptidoglycan-Binding Domain of Human Peptidoglycan Recognition Protein Ialpha, PDB code: 1sk3 was solved by R.Guan, E.L.Malchiodi, W.Qian, P.Schuck, R.A.Mariuzza, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.63 / 2.80
Space group P 32 2 1
Cell size a, b, c (Å), α, β, γ (°) 102.632, 102.632, 41.496, 90.00, 90.00, 120.00
R / Rfree (%) 21.9 / 25.3

Nickel Binding Sites:

The binding sites of Nickel atom in the Crystal Structure of the C-Terminal Peptidoglycan-Binding Domain of Human Peptidoglycan Recognition Protein Ialpha (pdb code 1sk3). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 2 binding sites of Nickel where determined in the Crystal Structure of the C-Terminal Peptidoglycan-Binding Domain of Human Peptidoglycan Recognition Protein Ialpha, PDB code: 1sk3:
Jump to Nickel binding site number: 1; 2;

Nickel binding site 1 out of 2 in 1sk3

Go back to Nickel Binding Sites List in 1sk3
Nickel binding site 1 out of 2 in the Crystal Structure of the C-Terminal Peptidoglycan-Binding Domain of Human Peptidoglycan Recognition Protein Ialpha


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 C-Terminal Peptidoglycan-Binding Domain of Human Peptidoglycan Recognition Protein Ialpha within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni21

b:28.4
occ:1.00
O A:VAL177 2.1 38.1 1.0
OD2 A:ASP296 2.1 33.9 1.0
O A:HOH1 2.5 28.4 1.0
N A:VAL177 2.6 38.1 1.0
C A:VAL177 2.8 38.1 1.0
CG A:ASP296 3.0 33.9 1.0
CA A:VAL177 3.2 38.1 1.0
OD1 A:ASP296 3.3 33.9 1.0
N A:CYS178 4.0 42.2 1.0
O A:ASP296 4.0 30.9 1.0
O A:HOH4 4.1 16.7 1.0
OE1 A:GLN299 4.3 26.7 1.0
CB A:ASP296 4.4 33.9 1.0
O A:HOH9 4.4 33.3 1.0
CA A:CYS178 4.5 42.2 1.0
CG2 A:VAL177 4.5 19.2 1.0
CB A:VAL177 4.5 19.2 1.0
CA A:ASP296 4.6 30.9 1.0
C A:ASP296 4.6 30.9 1.0
CB A:CYS300 4.8 50.4 1.0
C A:CYS178 4.8 42.2 1.0

Nickel binding site 2 out of 2 in 1sk3

Go back to Nickel Binding Sites List in 1sk3
Nickel binding site 2 out of 2 in the Crystal Structure of the C-Terminal Peptidoglycan-Binding Domain of Human Peptidoglycan Recognition Protein Ialpha


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 C-Terminal Peptidoglycan-Binding Domain of Human Peptidoglycan Recognition Protein Ialpha within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni22

b:27.8
occ:1.00
OE1 A:GLU292 2.8 57.9 1.0
OE2 A:GLU292 2.9 57.9 1.0
CD A:GLU292 2.9 57.9 1.0
CG A:GLU292 4.1 57.9 1.0
CB A:GLU292 4.8 57.9 1.0

Reference:

R.Guan, E.L.Malchiodi, W.Qian, P.Schuck, R.A.Mariuzza. Crystal Structure of the C-Terminal Peptidoglycan-Binding Domain of Human Peptidoglycan Recognition Protein Ialpha J.Biol.Chem. V. 279 31873 2004.
ISSN: ISSN 0021-9258
PubMed: 15140887
DOI: 10.1074/JBC.M404920200
Page generated: Thu Oct 29 06:15:34 2020
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