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

Protein crystallography data

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

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 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 2eav

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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 2eav

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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 2eav

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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 2eav

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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 2eav

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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 2eav

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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

Reference:

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
Page generated: Thu Oct 29 06:17:00 2020
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