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Nickel in PDB 4n0r: Crystal Structure of A Putative Glycoside Hydrolase (BVU_0362) From Bacteroides Vulgatus Atcc 8482 at 1.80 A Resolution

Protein crystallography data

The structure of Crystal Structure of A Putative Glycoside Hydrolase (BVU_0362) From Bacteroides Vulgatus Atcc 8482 at 1.80 A Resolution, PDB code: 4n0r was solved by Joint Center For Structural Genomics (Jcsg), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.21 / 1.80
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 226.439, 67.684, 90.066, 90.00, 90.00, 90.00
R / Rfree (%) 15 / 18

Nickel Binding Sites:

The binding sites of Nickel atom in the Crystal Structure of A Putative Glycoside Hydrolase (BVU_0362) From Bacteroides Vulgatus Atcc 8482 at 1.80 A Resolution (pdb code 4n0r). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 10 binding sites of Nickel where determined in the Crystal Structure of A Putative Glycoside Hydrolase (BVU_0362) From Bacteroides Vulgatus Atcc 8482 at 1.80 A Resolution, PDB code: 4n0r:
Jump to Nickel binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Nickel binding site 1 out of 10 in 4n0r

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Nickel binding site 1 out of 10 in the Crystal Structure of A Putative Glycoside Hydrolase (BVU_0362) From Bacteroides Vulgatus Atcc 8482 at 1.80 A Resolution


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 A Putative Glycoside Hydrolase (BVU_0362) From Bacteroides Vulgatus Atcc 8482 at 1.80 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni602

b:49.0
occ:1.00
 O2 A:UNL601 2.3 39.6 1.0
O3 A:UNL601 2.3 39.1 1.0
OE2 A:GLU276 2.4 14.9 1.0
O1 A:UNL601 2.5 23.8 1.0
OE1 A:GLN328 2.6 17.7 1.0
O A:HOH1334 2.8 39.6 1.0
O7 A:UNL601 2.8 40.6 1.0
O A:HOH1333 2.8 37.2 1.0
CD A:GLU276 3.1 19.6 1.0
O4 A:UNL601 3.1 43.6 1.0
NE2 A:GLN328 3.2 18.9 1.0
CD A:GLN328 3.3 19.5 1.0
OE1 A:GLU276 3.5 18.4 1.0
OE2 A:GLU354 3.6 15.9 1.0
O6 A:UNL601 3.8 38.1 1.0
OE1 A:GLU354 4.0 19.0 1.0
CD A:GLU354 4.1 19.5 1.0
O A:HOH779 4.2 23.6 1.0
CG A:GLU276 4.2 16.6 1.0
O A:HOH773 4.8 23.4 1.0
CG A:GLN328 4.8 19.6 1.0
O A:HOH906 4.8 26.9 1.0
CG A:TRP365 4.9 17.2 1.0
CD1 A:TRP365 5.0 23.5 1.0
CB A:TRP365 5.0 17.7 1.0

Nickel binding site 2 out of 10 in 4n0r

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Nickel binding site 2 out of 10 in the Crystal Structure of A Putative Glycoside Hydrolase (BVU_0362) From Bacteroides Vulgatus Atcc 8482 at 1.80 A Resolution


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 A Putative Glycoside Hydrolase (BVU_0362) From Bacteroides Vulgatus Atcc 8482 at 1.80 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni603

b:47.7
occ:1.00
 O A:HOH1188 1.8 33.6 1.0
O A:HOH1189 2.0 41.3 1.0
O A:HOH1190 2.2 55.6 1.0
NE2 A:HIS428 2.3 25.9 1.0
O A:HOH1192 2.5 41.2 1.0
CE1 A:HIS428 3.1 26.6 1.0
O A:HOH1191 3.2 50.8 1.0
CD2 A:HIS428 3.3 27.1 1.0
ND1 A:HIS428 4.2 24.1 1.0
CG A:HIS428 4.3 21.6 1.0
O A:HOH1090 4.7 32.4 1.0
O A:HOH963 4.9 39.8 1.0

Nickel binding site 3 out of 10 in 4n0r

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Nickel binding site 3 out of 10 in the Crystal Structure of A Putative Glycoside Hydrolase (BVU_0362) From Bacteroides Vulgatus Atcc 8482 at 1.80 A Resolution


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 A Putative Glycoside Hydrolase (BVU_0362) From Bacteroides Vulgatus Atcc 8482 at 1.80 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni604

b:62.1
occ:1.00
 NE2 A:HIS121 2.5 17.7 1.0
O A:HOH1206 2.7 47.7 1.0
O A:HOH1046 2.8 37.5 1.0
O A:HOH950 2.8 34.3 1.0
O A:HOH1050 2.9 31.8 1.0
CD2 A:HIS121 3.5 18.8 1.0
CE1 A:HIS121 3.5 22.2 1.0
OE1 A:GLU120 3.6 38.8 1.0
O A:HOH889 4.0 26.0 1.0
CE A:LYS344 4.2 19.9 1.0
O A:HOH1204 4.3 46.3 1.0
CD A:LYS344 4.4 20.0 1.0
ND1 A:HIS121 4.6 17.4 1.0
CG A:HIS121 4.6 15.7 1.0
O A:HOH1207 4.6 42.6 1.0
CD A:GLU120 4.8 26.0 1.0
O A:HOH1045 4.8 33.7 1.0
O A:HOH1007 4.9 26.7 1.0
NH1 A:ARG343 4.9 17.5 1.0

Nickel binding site 4 out of 10 in 4n0r

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Nickel binding site 4 out of 10 in the Crystal Structure of A Putative Glycoside Hydrolase (BVU_0362) From Bacteroides Vulgatus Atcc 8482 at 1.80 A Resolution


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 A Putative Glycoside Hydrolase (BVU_0362) From Bacteroides Vulgatus Atcc 8482 at 1.80 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni605

b:43.3
occ:1.00
 O A:HOH1127 1.8 32.3 1.0
O A:HOH1123 1.8 30.3 1.0
NE2 A:HIS112 2.2 26.7 1.0
O A:HOH1124 2.3 38.6 1.0
O A:HOH1126 2.5 23.4 0.5
O A:HOH1125 2.5 40.9 1.0
O A:HOH1129 2.5 39.7 1.0
CD2 A:HIS112 3.1 28.8 1.0
CE1 A:HIS112 3.3 29.7 1.0
OD1 A:ASP110 3.9 51.1 1.0
O A:HOH1128 4.1 46.2 1.0
O A:HOH1126 4.2 23.0 0.5
CG A:HIS112 4.3 26.6 1.0
ND1 A:HIS112 4.3 27.9 1.0
O A:ASP110 4.6 26.6 1.0
CA A:ASP110 4.6 33.8 1.0
CG A:ASP110 4.8 49.5 1.0
O A:LYS109 4.9 40.2 1.0
CB A:ASP110 4.9 49.0 1.0
C A:ASP110 4.9 28.6 1.0
O A:HOH1173 5.0 50.9 1.0

Nickel binding site 5 out of 10 in 4n0r

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Nickel binding site 5 out of 10 in the Crystal Structure of A Putative Glycoside Hydrolase (BVU_0362) From Bacteroides Vulgatus Atcc 8482 at 1.80 A Resolution


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 A Putative Glycoside Hydrolase (BVU_0362) From Bacteroides Vulgatus Atcc 8482 at 1.80 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni606

b:44.6
occ:0.50
 NE2 A:HIS514 2.3 25.2 1.0
O A:HOH1131 2.4 45.4 1.0
O A:HOH1130 2.4 33.2 1.0
CE1 A:HIS514 3.2 27.6 1.0
CD2 A:HIS514 3.3 27.2 1.0
O A:HOH1187 3.7 27.8 0.5
ND1 A:HIS514 4.3 25.2 1.0
CG A:HIS514 4.4 23.1 1.0
OE2 A:GLU501 4.6 25.9 0.5
CG2 A:ILE513 4.7 26.1 0.5
O A:HOH1187 4.8 30.2 0.5
OE1 A:GLU501 4.8 32.3 0.5
CG2 A:ILE513 5.0 22.6 0.5

Nickel binding site 6 out of 10 in 4n0r

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Nickel binding site 6 out of 10 in the Crystal Structure of A Putative Glycoside Hydrolase (BVU_0362) From Bacteroides Vulgatus Atcc 8482 at 1.80 A Resolution


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 A Putative Glycoside Hydrolase (BVU_0362) From Bacteroides Vulgatus Atcc 8482 at 1.80 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ni602

b:52.0
occ:1.00
 O2 B:UNL601 2.2 36.9 1.0
OE2 B:GLU276 2.3 17.9 1.0
O B:HOH1324 2.4 31.1 1.0
O1 B:UNL601 2.5 22.2 1.0
O7 B:UNL601 2.6 35.1 1.0
OE1 B:GLN328 2.7 17.3 1.0
O3 B:UNL601 2.8 46.2 1.0
CD B:GLU276 3.0 17.9 1.0
O B:HOH1323 3.0 40.7 1.0
NE2 B:GLN328 3.2 18.4 1.0
O4 B:UNL601 3.3 40.6 1.0
CD B:GLN328 3.3 20.6 1.0
OE1 B:GLU276 3.5 21.5 1.0
OE2 B:GLU354 3.6 16.4 1.0
O6 B:UNL601 3.9 36.9 1.0
OE1 B:GLU354 4.0 17.7 1.0
O B:HOH799 4.0 23.3 1.0
CD B:GLU354 4.1 19.5 1.0
CG B:GLU276 4.1 17.5 1.0
O B:HOH780 4.6 27.3 1.0
O B:HOH778 4.7 20.8 1.0
CG B:GLN328 4.8 13.9 1.0
CG B:TRP365 4.9 18.7 1.0
CD1 B:TRP365 5.0 20.2 1.0
CB B:TRP365 5.0 18.2 1.0
OH B:TYR237 5.0 16.8 1.0

Nickel binding site 7 out of 10 in 4n0r

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Nickel binding site 7 out of 10 in the Crystal Structure of A Putative Glycoside Hydrolase (BVU_0362) From Bacteroides Vulgatus Atcc 8482 at 1.80 A Resolution


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 7 of Crystal Structure of A Putative Glycoside Hydrolase (BVU_0362) From Bacteroides Vulgatus Atcc 8482 at 1.80 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ni603

b:67.4
occ:1.00
 NE2 B:HIS121 2.5 17.9 1.0
O B:HOH1135 2.7 40.8 1.0
O B:HOH1133 2.9 31.3 1.0
O B:HOH1136 3.0 38.6 1.0
O B:HOH862 3.1 32.3 1.0
CE1 B:HIS121 3.5 21.2 1.0
CD2 B:HIS121 3.5 17.8 1.0
OE1 B:GLU120 3.6 35.6 1.0
O B:HOH882 4.0 31.4 1.0
CE B:LYS344 4.2 19.3 1.0
CD B:LYS344 4.3 17.4 1.0
ND1 B:HIS121 4.6 17.0 1.0
CG B:HIS121 4.6 17.9 1.0
CD B:GLU120 4.8 30.8 1.0
NH1 B:ARG343 4.8 17.9 1.0
O B:HOH942 4.9 31.1 1.0
O B:HOH872 5.0 38.0 1.0

Nickel binding site 8 out of 10 in 4n0r

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Nickel binding site 8 out of 10 in the Crystal Structure of A Putative Glycoside Hydrolase (BVU_0362) From Bacteroides Vulgatus Atcc 8482 at 1.80 A Resolution


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 8 of Crystal Structure of A Putative Glycoside Hydrolase (BVU_0362) From Bacteroides Vulgatus Atcc 8482 at 1.80 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ni604

b:44.2
occ:1.00
 O B:HOH1180 1.8 33.7 1.0
O B:HOH1155 1.8 33.5 1.0
NE2 B:HIS112 2.3 27.4 1.0
O B:HOH1157 2.4 45.8 1.0
O B:HOH1152 2.4 39.4 1.0
O B:HOH1154 2.6 48.9 1.0
O B:HOH1153 2.6 40.9 1.0
O B:HOH1156 2.6 37.4 1.0
CD2 B:HIS112 3.1 25.9 1.0
CE1 B:HIS112 3.3 30.6 1.0
OD1 B:ASP110 4.0 39.6 1.0
CG B:HIS112 4.3 27.5 1.0
ND1 B:HIS112 4.3 25.9 1.0
O B:ASP110 4.6 28.0 1.0
CA B:ASP110 4.7 29.7 1.0
O B:LYS109 4.9 34.7 1.0
CG B:ASP110 4.9 46.6 1.0

Nickel binding site 9 out of 10 in 4n0r

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Nickel binding site 9 out of 10 in the Crystal Structure of A Putative Glycoside Hydrolase (BVU_0362) From Bacteroides Vulgatus Atcc 8482 at 1.80 A Resolution


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 9 of Crystal Structure of A Putative Glycoside Hydrolase (BVU_0362) From Bacteroides Vulgatus Atcc 8482 at 1.80 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ni605

b:63.5
occ:1.00
 O B:HOH1226 2.3 50.9 1.0
NE2 B:HIS514 2.6 30.6 1.0
CD2 B:HIS514 3.2 26.7 1.0
CE1 B:HIS514 3.8 32.9 1.0
O B:HOH1177 3.9 41.6 1.0
CG B:HIS514 4.4 27.9 1.0
CD1 B:ILE513 4.5 50.5 1.0
ND1 B:HIS514 4.7 28.4 1.0

Nickel binding site 10 out of 10 in 4n0r

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Nickel binding site 10 out of 10 in the Crystal Structure of A Putative Glycoside Hydrolase (BVU_0362) From Bacteroides Vulgatus Atcc 8482 at 1.80 A Resolution


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 10 of Crystal Structure of A Putative Glycoside Hydrolase (BVU_0362) From Bacteroides Vulgatus Atcc 8482 at 1.80 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ni606

b:53.0
occ:1.00
 O B:HOH1174 2.1 46.7 1.0
O B:HOH1181 2.1 54.3 1.0
NE2 B:HIS428 2.2 31.1 1.0
O B:HOH1173 2.5 47.6 1.0
O B:HOH1172 2.5 47.3 1.0
O B:HOH1171 2.7 49.8 1.0
O B:HOH1175 2.8 43.2 1.0
CE1 B:HIS428 3.1 30.3 1.0
CD2 B:HIS428 3.3 29.4 1.0
ND1 B:HIS428 4.2 28.4 1.0
CG B:HIS428 4.3 27.7 1.0
O B:HOH977 5.0 29.3 1.0

Reference:

Joint Center For Structural Genomics (Jcsg), Joint Center For Structural Genomics (Jcsg). N/A N/A.
Page generated: Mon Aug 18 19:32:31 2025

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