Atomistry » Nickel » PDB 4lto-4ofl » 4n0r
Atomistry »
  Nickel »
    PDB 4lto-4ofl »
      4n0r »

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

Go back to Nickel Binding Sites List in 4n0r
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

Go back to Nickel Binding Sites List in 4n0r
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

Go back to Nickel Binding Sites List in 4n0r
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

Go back to Nickel Binding Sites List in 4n0r
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

Go back to Nickel Binding Sites List in 4n0r
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

Go back to Nickel Binding Sites List in 4n0r
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

Go back to Nickel Binding Sites List in 4n0r
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

Go back to Nickel Binding Sites List in 4n0r
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

Go back to Nickel Binding Sites List in 4n0r
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

Go back to Nickel Binding Sites List in 4n0r
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: Wed Oct 9 18:33:41 2024

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy