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Nickel in PDB 1xm5: Crystal Structure of Metal-Dependent Hydrolase Ybey From E. Coli, Pfam UPF0054

Protein crystallography data

The structure of Crystal Structure of Metal-Dependent Hydrolase Ybey From E. Coli, Pfam UPF0054, PDB code: 1xm5 was solved by A.A.Fedorov, E.V.Fedorov, W.Shi, U.A.Ramagopal, R.Thirumuruhan, S.C.Almo, S.K.Burley, New York Sgx Research Center Forstructural Genomics (Nysgxrc), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 25.00 / 2.70
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 46.073, 119.613, 132.903, 90.00, 90.00, 90.00
R / Rfree (%) 23.4 / 27.3

Nickel Binding Sites:

The binding sites of Nickel atom in the Crystal Structure of Metal-Dependent Hydrolase Ybey From E. Coli, Pfam UPF0054 (pdb code 1xm5). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 4 binding sites of Nickel where determined in the Crystal Structure of Metal-Dependent Hydrolase Ybey From E. Coli, Pfam UPF0054, PDB code: 1xm5:
Jump to Nickel binding site number: 1; 2; 3; 4;

Nickel binding site 1 out of 4 in 1xm5

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Nickel binding site 1 out of 4 in the Crystal Structure of Metal-Dependent Hydrolase Ybey From E. Coli, Pfam UPF0054


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 Metal-Dependent Hydrolase Ybey From E. Coli, Pfam UPF0054 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni5001

b:49.5
occ:1.00
NE2 A:HIS1124 2.1 80.5 1.0
NE2 A:HIS1114 2.2 65.5 1.0
NE2 A:HIS1118 2.2 40.8 1.0
CE1 A:HIS1124 3.0 81.2 1.0
CD2 A:HIS1118 3.1 41.1 1.0
CD2 A:HIS1114 3.2 60.8 1.0
CE1 A:HIS1114 3.2 62.3 1.0
CD2 A:HIS1124 3.2 81.9 1.0
CE1 A:HIS1118 3.3 43.3 1.0
ND1 A:HIS1124 4.2 81.9 1.0
CG A:HIS1118 4.3 41.2 1.0
ND1 A:HIS1114 4.3 60.6 1.0
CG A:HIS1114 4.3 58.3 1.0
CG A:HIS1124 4.3 82.3 1.0
ND1 A:HIS1118 4.3 42.6 1.0

Nickel binding site 2 out of 4 in 1xm5

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Nickel binding site 2 out of 4 in the Crystal Structure of Metal-Dependent Hydrolase Ybey From E. Coli, Pfam UPF0054


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 Metal-Dependent Hydrolase Ybey From E. Coli, Pfam UPF0054 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ni5002

b:48.6
occ:1.00
NE2 B:HIS2124 2.1 66.8 1.0
NE2 B:HIS2118 2.1 35.6 1.0
NE2 B:HIS2114 2.3 43.2 1.0
CE1 B:HIS2124 2.9 67.5 1.0
CD2 B:HIS2118 3.1 38.9 1.0
CD2 B:HIS2124 3.2 69.0 1.0
CE1 B:HIS2118 3.2 35.5 1.0
CE1 B:HIS2114 3.2 43.7 1.0
CD2 B:HIS2114 3.2 44.4 1.0
ND1 B:HIS2124 4.1 67.8 1.0
CG B:HIS2118 4.2 39.6 1.0
ND1 B:HIS2118 4.2 38.7 1.0
CG B:HIS2124 4.2 69.7 1.0
ND1 B:HIS2114 4.3 45.8 1.0
CG B:HIS2114 4.4 44.4 1.0

Nickel binding site 3 out of 4 in 1xm5

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Nickel binding site 3 out of 4 in the Crystal Structure of Metal-Dependent Hydrolase Ybey From E. Coli, Pfam UPF0054


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 Metal-Dependent Hydrolase Ybey From E. Coli, Pfam UPF0054 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ni5003

b:61.1
occ:1.00
NE2 C:HIS3114 2.2 83.5 1.0
NE2 C:HIS3118 2.2 40.0 1.0
NE2 C:HIS3124 2.2 90.7 1.0
CD2 C:HIS3118 3.0 42.2 1.0
CE1 C:HIS3124 3.1 92.2 1.0
CD2 C:HIS3114 3.1 81.5 1.0
CE1 C:HIS3114 3.2 83.1 1.0
CD2 C:HIS3124 3.3 91.8 1.0
CE1 C:HIS3118 3.3 40.9 1.0
CG C:HIS3118 4.2 41.7 1.0
ND1 C:HIS3124 4.2 93.1 1.0
ND1 C:HIS3114 4.2 82.2 1.0
CG C:HIS3114 4.2 80.7 1.0
ND1 C:HIS3118 4.3 40.0 1.0
CG C:HIS3124 4.4 93.3 1.0

Nickel binding site 4 out of 4 in 1xm5

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Nickel binding site 4 out of 4 in the Crystal Structure of Metal-Dependent Hydrolase Ybey From E. Coli, Pfam UPF0054


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 Metal-Dependent Hydrolase Ybey From E. Coli, Pfam UPF0054 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ni5004

b:54.6
occ:1.00
NE2 D:HIS4124 2.0 49.8 1.0
NE2 D:HIS4114 2.0 42.0 1.0
NE2 D:HIS4118 2.3 50.6 1.0
CE1 D:HIS4124 2.6 51.0 1.0
CE1 D:HIS4114 2.9 41.4 1.0
CE1 D:HIS4118 3.1 50.0 1.0
CD2 D:HIS4114 3.1 44.7 1.0
CD2 D:HIS4118 3.2 47.9 1.0
CD2 D:HIS4124 3.3 51.7 1.0
ND1 D:HIS4124 3.8 53.3 1.0
ND1 D:HIS4114 4.1 42.9 1.0
ND1 D:HIS4118 4.2 49.8 1.0
CG D:HIS4124 4.2 54.4 1.0
CG D:HIS4114 4.2 45.1 1.0
CG D:HIS4118 4.3 48.7 1.0
CE D:MET4133 5.0 49.8 1.0

Reference:

C.Zhan, E.V.Fedorov, W.Shi, U.A.Ramagopal, R.Thirumuruhan, B.A.Manjasetty, S.C.Almo, A.Fiser, M.R.Chance, A.A.Fedorov. The Ybey Protein From Escherichia Coli Is A Metalloprotein. Acta Crystallogr.,Sect.F V. 61 959 2005.
ISSN: ESSN 1744-3091
PubMed: 16511207
DOI: 10.1107/S1744309105031131
Page generated: Fri Sep 25 08:04:04 2020
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