Nickel in PDB 2eav: Crystal Structure of the C-Terminal Peptidoglycan-Binding Domain of Human Peptidoglycan Recognition Protein Ibeta

The structure of Crystal Structure of the C-Terminal Peptidoglycan-Binding Domain of Human Peptidoglycan Recognition Protein Ibeta, PDB code: 2eav was solved by S.Cho, R.A.Mariuzza, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.00 / 2.20
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	127.435, 56.785, 36.761, 90.00, 90.00, 90.00
R / Rfree (%)	22.9 / 28.5

The binding sites of Nickel atom in the Crystal Structure of the C-Terminal Peptidoglycan-Binding Domain of Human Peptidoglycan Recognition Protein Ibeta (pdb code 2eav). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 6 binding sites of Nickel where determined in the Crystal Structure of the C-Terminal Peptidoglycan-Binding Domain of Human Peptidoglycan Recognition Protein Ibeta, PDB code: 2eav:
Jump to Nickel binding site number: 1; 2; 3; 4; 5; 6;

Nickel binding site 1 out of 6 in the Crystal Structure of the C-Terminal Peptidoglycan-Binding Domain of Human Peptidoglycan Recognition Protein Ibeta


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 Ibeta within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni501 b:35.8 occ:1.00 NE2 B:HIS370 2.1 33.9 1.0 OD1 A:ASP328 2.2 26.0 1.0 CE1 B:HIS370 3.0 32.9 1.0 N A:CYS210 3.1 26.2 1.0 CG A:ASP328 3.1 22.2 1.0 CD2 B:HIS370 3.3 32.9 1.0 OD2 A:ASP328 3.4 23.9 1.0 CA A:CYS210 3.9 28.8 1.0 ND1 B:HIS370 4.1 32.1 1.0 O A:HOH19 4.3 16.1 1.0 CG B:HIS370 4.3 32.1 1.0 C A:CYS210 4.4 27.8 1.0 CB A:ASP328 4.5 21.5 1.0 O B:PRO341 4.6 31.9 1.0 O A:ASP328 4.6 20.4 1.0 N A:PRO211 4.7 26.9 1.0 CA A:ASP328 4.8 21.1 1.0 CD A:PRO211 4.8 26.7 1.0 OE1 A:GLN331 4.9 28.4 1.0

Nickel binding site 2 out of 6 in the Crystal Structure of the C-Terminal Peptidoglycan-Binding Domain of Human Peptidoglycan Recognition Protein Ibeta


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 Ibeta within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni504 b:61.8 occ:1.00 OE2 B:GLU324 2.6 25.9 1.0 OE1 B:GLU324 2.6 29.3 1.0 CE1 A:HIS373 2.8 55.2 1.0 CD B:GLU324 2.9 28.6 1.0 NE2 A:HIS373 3.2 55.3 1.0 ND1 A:HIS373 3.5 54.5 1.0 CD2 A:HIS373 4.0 53.8 1.0 O A:HOH110 4.1 41.3 1.0 O A:PHE371 4.1 33.1 1.0 CG A:HIS373 4.2 53.9 1.0 CG B:GLU324 4.4 24.7 1.0

Nickel binding site 3 out of 6 in the Crystal Structure of the C-Terminal Peptidoglycan-Binding Domain of Human Peptidoglycan Recognition Protein Ibeta


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 C-Terminal Peptidoglycan-Binding Domain of Human Peptidoglycan Recognition Protein Ibeta within 5.0Å range: probe atom residue distance (Å) B Occ B:Ni500 b:30.6 occ:1.00 NE2 A:HIS370 2.1 18.8 1.0 OD2 B:ASP328 2.1 24.1 1.0 NE2 B:GLN331 2.3 19.2 1.0 O B:HOH114 2.6 39.2 1.0 CE1 A:HIS370 2.9 16.3 1.0 CG B:ASP328 2.9 24.9 1.0 OD1 B:ASP328 3.1 25.9 1.0 CD2 A:HIS370 3.2 19.0 1.0 CD B:GLN331 3.3 21.7 1.0 OE1 B:GLN331 3.6 22.2 1.0 N B:CYS210 3.8 25.5 1.0 ND1 A:HIS370 4.0 20.5 1.0 CG A:HIS370 4.2 21.6 1.0 CE A:MET334 4.4 37.4 1.0 CB B:ASP328 4.4 23.6 1.0 CG B:GLN331 4.5 22.6 1.0 CA B:CYS210 4.6 25.4 1.0 O A:PRO341 4.7 26.8 1.0 C B:CYS210 4.8 25.2 1.0 CA B:ASP328 4.9 23.2 1.0 O B:ASP328 4.9 24.5 1.0 N B:PRO211 4.9 23.7 1.0

Nickel binding site 4 out of 6 in the Crystal Structure of the C-Terminal Peptidoglycan-Binding Domain of Human Peptidoglycan Recognition Protein Ibeta


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 4 of Crystal Structure of the C-Terminal Peptidoglycan-Binding Domain of Human Peptidoglycan Recognition Protein Ibeta within 5.0Å range: probe atom residue distance (Å) B Occ B:Ni502 b:39.9 occ:1.00 ND1 B:HIS348 1.8 33.0 1.0 CE1 B:HIS348 2.2 35.1 1.0 O B:HOH41 2.6 31.3 1.0 CG2 B:ILE239 2.8 29.9 1.0 OG B:SER356 3.0 45.8 1.0 CG B:HIS348 3.1 33.2 1.0 CD1 B:ILE239 3.4 27.6 1.0 NE2 B:HIS348 3.5 35.6 1.0 CG1 B:ILE239 3.6 32.1 1.0 CB B:ILE239 3.8 29.6 1.0 CD2 B:HIS348 3.9 34.7 1.0 CB B:HIS348 3.9 31.0 1.0 CB B:SER356 4.0 51.8 1.0 O B:SER296 4.4 28.6 1.0 OH B:TYR274 4.5 23.6 1.0 CE2 B:TYR274 4.6 20.1 1.0 O B:HIS240 4.6 36.2 1.0 CA B:ILE239 4.7 30.1 1.0 O B:HOH119 4.8 38.4 1.0 N B:HIS240 4.9 31.1 1.0 CB B:SER296 5.0 28.9 1.0

Nickel binding site 5 out of 6 in the Crystal Structure of the C-Terminal Peptidoglycan-Binding Domain of Human Peptidoglycan Recognition Protein Ibeta


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 5 of Crystal Structure of the C-Terminal Peptidoglycan-Binding Domain of Human Peptidoglycan Recognition Protein Ibeta within 5.0Å range: probe atom residue distance (Å) B Occ B:Ni503 b:15.7 occ:1.00 O B:GLY299 3.9 27.9 1.0 OD2 B:ASP302 4.2 22.5 1.0 O B:HOH87 4.2 27.0 1.0 OD1 B:ASP302 4.4 26.8 1.0 CG B:ASP302 4.7 23.4 1.0 CD1 B:ILE303 4.9 22.9 1.0

Nickel binding site 6 out of 6 in the Crystal Structure of the C-Terminal Peptidoglycan-Binding Domain of Human Peptidoglycan Recognition Protein Ibeta


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 6 of Crystal Structure of the C-Terminal Peptidoglycan-Binding Domain of Human Peptidoglycan Recognition Protein Ibeta within 5.0Å range: probe atom residue distance (Å) B Occ B:Ni505 b:47.5 occ:1.00 NE2 B:HIS373 2.4 67.2 1.0 CD2 B:HIS373 3.2 65.8 1.0 CE1 B:HIS373 3.2 66.2 1.0 OE1 A:GLU324 3.3 36.3 1.0 O B:PHE371 3.3 38.1 1.0 CD A:GLU324 3.7 37.2 1.0 OE2 A:GLU324 3.8 38.3 1.0 ND1 B:HIS373 4.2 65.3 1.0 CG B:HIS373 4.2 64.7 1.0 C B:PHE371 4.4 38.1 1.0 N B:PHE371 4.6 32.4 1.0 CB A:GLU324 4.8 28.3 1.0 CG A:GLU324 4.9 33.9 1.0 O A:HOH86 4.9 25.9 1.0 CA B:PHE371 5.0 35.1 1.0

S.Cho, Q.Wang, C.P.Swaminathan, D.Hesek, M.Lee, G.J.Boons, S.Mobashery, R.A.Mariuzza. Structural Insights Into the Bactericidal Mechanism of Human Peptidoglycan Recognition Proteins Proc.Natl.Acad.Sci.Usa V. 104 8761 2007.
ISSN: ISSN 0027-8424
PubMed: 17502600
DOI: 10.1073/PNAS.0701453104