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Arsenic in PDB 2vqg: Crystal Structure of Porb From Corynebacterium Glutamicum ( Crystal Form I)

Protein crystallography data

The structure of Crystal Structure of Porb From Corynebacterium Glutamicum ( Crystal Form I), PDB code: 2vqg was solved by K.Ziegler, R.Benz, G.E.Schulz, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 72.36 / 1.82
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 87.070, 87.070, 260.530, 90.00, 90.00, 90.00
R / Rfree (%) 19.5 / 21.5

Other elements in 2vqg:

The structure of Crystal Structure of Porb From Corynebacterium Glutamicum ( Crystal Form I) also contains other interesting chemical elements:

Zinc (Zn) 42 atoms

Arsenic Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 13;

Binding sites:

The binding sites of Arsenic atom in the Crystal Structure of Porb From Corynebacterium Glutamicum ( Crystal Form I) (pdb code 2vqg). This binding sites where shown within 5.0 Angstroms radius around Arsenic atom.
In total 13 binding sites of Arsenic where determined in the Crystal Structure of Porb From Corynebacterium Glutamicum ( Crystal Form I), PDB code: 2vqg:
Jump to Arsenic binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Arsenic binding site 1 out of 13 in 2vqg

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Arsenic binding site 1 out of 13 in the Crystal Structure of Porb From Corynebacterium Glutamicum ( Crystal Form I)


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Stereo pair view

A full contact list of Arsenic with other atoms in the As binding site number 1 of Crystal Structure of Porb From Corynebacterium Glutamicum ( Crystal Form I) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:As1092

b:67.0
occ:0.90
 AS A:CAC1092 0.0 67.0 0.9
O2 A:CAC1092 1.7 64.8 0.9
O1 A:CAC1092 1.7 65.8 0.9
C1 A:CAC1092 2.0 66.0 0.9
C2 A:CAC1092 2.0 65.7 0.9
ZN A:ZN1089 3.0 11.1 0.9
OE1 A:GLU37 3.0 41.9 1.0
ZN A:ZN1090 3.4 54.3 0.9
NZ A:LYS30 3.7 13.6 1.0
C1 A:CAC1093 3.9 61.7 0.9
O1 A:CAC1093 3.9 60.9 0.9
OE2 A:GLU26 4.1 15.6 1.0
CD A:GLU37 4.2 39.6 1.0
CE A:LYS30 4.2 15.3 1.0
AS A:CAC1093 4.2 63.4 0.9
O F:GLY82 4.3 18.0 1.0
O2 A:CAC1093 4.3 60.9 0.9
OE2 F:GLU26 4.3 13.4 1.0
OE2 A:GLU37 4.6 41.2 1.0
OE1 F:GLU26 4.8 14.8 1.0
CD F:GLU26 4.9 14.2 1.0

Arsenic binding site 2 out of 13 in 2vqg

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Arsenic binding site 2 out of 13 in the Crystal Structure of Porb From Corynebacterium Glutamicum ( Crystal Form I)


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Stereo pair view

A full contact list of Arsenic with other atoms in the As binding site number 2 of Crystal Structure of Porb From Corynebacterium Glutamicum ( Crystal Form I) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:As1093

b:63.4
occ:0.90
 AS A:CAC1093 0.0 63.4 0.9
O2 A:CAC1093 1.7 60.9 0.9
O1 A:CAC1093 1.7 60.9 0.9
C2 A:CAC1093 2.0 62.0 0.9
C1 A:CAC1093 2.0 61.7 0.9
ZN A:ZN1089 2.9 11.1 0.9
OE1 F:GLU37 3.3 42.3 1.0
ZN A:ZN1090 3.4 54.3 0.9
O1 A:CAC1092 3.6 65.8 0.9
NZ F:LYS30 3.6 12.2 1.0
OE2 F:GLU26 3.9 13.4 1.0
O2 A:CAC1092 4.0 64.8 0.9
OE2 A:GLU26 4.1 15.6 1.0
CE F:LYS30 4.1 14.8 1.0
AS A:CAC1092 4.2 67.0 0.9
O A:GLY82 4.4 18.5 1.0
CD F:GLU37 4.5 39.6 1.0
C2 A:CAC1092 4.5 65.7 0.9
OE1 A:GLU26 4.7 13.3 1.0
O A:HOH2007 4.7 37.3 1.0
CD A:GLU26 4.8 13.4 1.0
OE2 F:GLU37 4.9 41.9 1.0
CD2 A:LEU83 5.0 20.1 1.0

Arsenic binding site 3 out of 13 in 2vqg

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Arsenic binding site 3 out of 13 in the Crystal Structure of Porb From Corynebacterium Glutamicum ( Crystal Form I)


Mono view


Stereo pair view

A full contact list of Arsenic with other atoms in the As binding site number 3 of Crystal Structure of Porb From Corynebacterium Glutamicum ( Crystal Form I) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:As1096

b:43.3
occ:0.50
 AS A:CAC1096 0.0 43.3 0.5
O2 A:CAC1096 1.7 43.2 0.5
O1 A:CAC1096 1.7 43.4 0.5
C1 A:CAC1096 2.0 43.5 0.5
C2 A:CAC1096 2.0 43.4 0.5
ZN A:ZN1099 2.9 31.9 0.5
ZN A:ZN1098 3.1 36.1 0.5
ZN A:ZN1094 3.2 37.4 0.5
OE1 A:GLU36 3.3 41.4 1.0
O1 A:CAC1097 3.4 38.4 0.5
O A:GLY33 3.9 19.6 1.0
CD A:GLU36 4.1 38.1 1.0
OE2 A:GLU36 4.6 39.9 1.0
O A:VAL34 4.6 20.3 1.0
O A:HOH2047 4.6 41.4 1.0
CB A:ALA47 4.7 16.2 1.0
CA A:VAL34 5.0 19.1 1.0
C A:VAL34 5.0 19.7 1.0
C A:GLY33 5.0 19.1 1.0
CG A:GLU36 5.0 32.8 1.0

Arsenic binding site 4 out of 13 in 2vqg

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Arsenic binding site 4 out of 13 in the Crystal Structure of Porb From Corynebacterium Glutamicum ( Crystal Form I)


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Stereo pair view

A full contact list of Arsenic with other atoms in the As binding site number 4 of Crystal Structure of Porb From Corynebacterium Glutamicum ( Crystal Form I) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:As1097

b:39.3
occ:0.50
 AS A:CAC1097 0.0 39.3 0.5
O1 A:CAC1097 1.7 38.4 0.5
O2 A:CAC1097 1.7 39.0 0.5
C1 A:CAC1097 2.0 38.7 0.5
C2 A:CAC1097 2.0 38.1 0.5
ZN A:ZN1094 3.0 37.4 0.5
ZN A:ZN1098 3.2 36.1 0.5
ZN A:ZN1099 3.4 31.9 0.5
O A:HOH2046 3.5 40.9 1.0
OE1 A:GLU36 3.8 41.4 1.0
O1 A:CAC1096 4.0 43.4 0.5
O A:HOH2044 4.0 45.8 1.0
O A:HOH2047 4.0 41.4 1.0
CD A:GLU36 4.5 38.1 1.0
O2 A:CAC1096 4.5 43.2 0.5
OE2 A:GLU36 4.6 39.9 1.0
O A:HOH2045 4.8 27.8 0.5

Arsenic binding site 5 out of 13 in 2vqg

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Arsenic binding site 5 out of 13 in the Crystal Structure of Porb From Corynebacterium Glutamicum ( Crystal Form I)


Mono view


Stereo pair view

A full contact list of Arsenic with other atoms in the As binding site number 5 of Crystal Structure of Porb From Corynebacterium Glutamicum ( Crystal Form I) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:As1092

b:28.8
occ:0.90
 AS B:CAC1092 0.0 28.8 0.9
O1 B:CAC1092 1.7 29.5 0.9
O2 B:CAC1092 1.8 24.1 0.9
C2 B:CAC1092 2.0 29.8 0.9
C1 B:CAC1092 2.0 30.7 0.9
ZN B:ZN1089 3.2 21.4 0.9
ZN B:ZN1088 3.3 10.2 0.9
OE1 E:GLU37 3.7 31.4 1.0
O2 B:CAC1093 3.9 18.1 0.9
O1 B:CAC1093 4.0 24.3 0.9
OE2 B:GLU26 4.0 13.6 1.0
NZ E:LYS30 4.3 20.0 1.0
OE1 B:GLU26 4.4 11.5 1.0
O B:HOH2014 4.4 36.0 1.0
CD B:GLU26 4.5 11.3 1.0
AS B:CAC1093 4.6 20.5 0.9
O B:GLY82 4.6 18.7 1.0
OE2 B:GLU37 4.7 35.8 1.0
OE2 E:GLU26 4.7 13.5 1.0
OE1 B:GLU37 4.7 36.6 1.0
CD2 B:LEU83 4.8 16.2 1.0
CD E:GLU37 4.8 28.1 1.0
CA B:LEU83 5.0 16.4 1.0

Arsenic binding site 6 out of 13 in 2vqg

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Arsenic binding site 6 out of 13 in the Crystal Structure of Porb From Corynebacterium Glutamicum ( Crystal Form I)


Mono view


Stereo pair view

A full contact list of Arsenic with other atoms in the As binding site number 6 of Crystal Structure of Porb From Corynebacterium Glutamicum ( Crystal Form I) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:As1093

b:20.5
occ:0.90
 AS B:CAC1093 0.0 20.5 0.9
O1 B:CAC1093 1.7 24.3 0.9
O2 B:CAC1093 1.8 18.1 0.9
C1 B:CAC1093 2.0 23.0 0.9
C2 B:CAC1093 2.0 23.2 0.9
ZN B:ZN1088 3.2 10.2 0.9
ZN B:ZN1089 3.3 21.4 0.9
OE1 B:GLU37 3.7 36.6 1.0
O2 B:CAC1092 4.0 24.1 0.9
OE2 E:GLU26 4.0 13.5 1.0
O1 B:CAC1092 4.0 29.5 0.9
O E:HOH2019 4.0 30.6 1.0
NZ B:LYS30 4.4 31.0 1.0
CD E:GLU26 4.5 10.7 1.0
OE1 E:GLU26 4.6 11.7 1.0
AS B:CAC1092 4.6 28.8 0.9
OE2 B:GLU26 4.6 13.6 1.0
O E:LEU83 4.7 13.3 1.0
OE1 E:GLU37 4.7 31.4 1.0
O E:GLY82 4.8 15.8 1.0
CD B:GLU37 4.8 34.1 1.0
OE2 E:GLU37 4.9 33.1 1.0
CA E:LEU83 4.9 14.2 1.0

Arsenic binding site 7 out of 13 in 2vqg

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Arsenic binding site 7 out of 13 in the Crystal Structure of Porb From Corynebacterium Glutamicum ( Crystal Form I)


Mono view


Stereo pair view

A full contact list of Arsenic with other atoms in the As binding site number 7 of Crystal Structure of Porb From Corynebacterium Glutamicum ( Crystal Form I) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:As1095

b:22.2
occ:1.00
 AS C:CAC1095 0.0 22.2 1.0
O2 C:CAC1095 1.7 26.0 1.0
O1 C:CAC1095 1.8 19.2 1.0
C2 C:CAC1095 1.9 24.2 1.0
C1 C:CAC1095 2.0 22.7 1.0
ZN C:ZN1091 3.2 11.2 1.0
ZN C:ZN1092 3.2 22.3 1.0
O H:HOH2017 3.5 43.0 1.0
OE1 H:GLU37 3.7 34.5 1.0
O1 C:CAC1101 3.9 20.2 1.0
OE2 C:GLU26 3.9 12.3 1.0
O C:HOH2014 3.9 25.2 1.0
O2 C:CAC1101 4.0 25.2 1.0
O C:HOH2013 4.0 41.5 1.0
NZ H:LYS30 4.3 30.9 1.0
CD C:GLU26 4.4 9.8 1.0
OE1 C:GLU26 4.5 11.9 1.0
AS C:CAC1101 4.6 23.9 1.0
OE1 C:GLU37 4.6 33.4 1.0
OE2 H:GLU26 4.7 12.9 1.0
O C:LEU83 4.8 12.9 1.0
OE2 C:GLU37 4.8 34.4 1.0
O C:GLY82 4.8 14.1 1.0
CD H:GLU37 4.8 31.4 1.0
CA C:LEU83 5.0 12.6 1.0

Arsenic binding site 8 out of 13 in 2vqg

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Arsenic binding site 8 out of 13 in the Crystal Structure of Porb From Corynebacterium Glutamicum ( Crystal Form I)


Mono view


Stereo pair view

A full contact list of Arsenic with other atoms in the As binding site number 8 of Crystal Structure of Porb From Corynebacterium Glutamicum ( Crystal Form I) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:As1098

b:40.1
occ:0.50
 AS C:CAC1098 0.0 40.1 0.5
O2 C:CAC1098 1.7 38.0 0.5
O1 C:CAC1098 1.7 39.3 0.5
C2 C:CAC1098 2.0 39.4 0.5
C1 C:CAC1098 2.0 39.6 0.5
ZN C:ZN1100 3.1 33.2 0.5
ZN C:ZN1096 3.4 36.5 0.5
ZN C:ZN1094 3.6 38.3 0.5
OE2 C:GLU53 3.8 30.8 1.0
O1 C:CAC1099 4.0 36.9 0.5
OE2 C:GLU68 4.2 35.1 1.0
CD C:GLU53 4.5 25.7 1.0
O2 C:CAC1099 4.7 36.4 0.5
CB C:ALA49 4.9 12.4 1.0
OE1 C:GLU53 4.9 27.9 1.0
AS C:CAC1099 5.0 36.9 0.5

Arsenic binding site 9 out of 13 in 2vqg

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Arsenic binding site 9 out of 13 in the Crystal Structure of Porb From Corynebacterium Glutamicum ( Crystal Form I)


Mono view


Stereo pair view

A full contact list of Arsenic with other atoms in the As binding site number 9 of Crystal Structure of Porb From Corynebacterium Glutamicum ( Crystal Form I) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:As1099

b:36.9
occ:0.50
 AS C:CAC1099 0.0 36.9 0.5
O2 C:CAC1099 1.7 36.4 0.5
O1 C:CAC1099 1.7 36.9 0.5
C1 C:CAC1099 2.0 36.4 0.5
C2 C:CAC1099 2.0 36.7 0.5
ZN C:ZN1096 2.7 36.5 0.5
ZN C:ZN1094 3.1 38.3 0.5
ZN C:ZN1100 3.4 33.2 0.5
O1 C:CAC1098 4.1 39.3 0.5
O2 C:CAC1098 4.3 38.0 0.5
OE1 C:GLU53 4.5 27.9 1.0
OE2 C:GLU53 4.7 30.8 1.0
AS C:CAC1098 5.0 40.1 0.5

Arsenic binding site 10 out of 13 in 2vqg

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Arsenic binding site 10 out of 13 in the Crystal Structure of Porb From Corynebacterium Glutamicum ( Crystal Form I)


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Stereo pair view

A full contact list of Arsenic with other atoms in the As binding site number 10 of Crystal Structure of Porb From Corynebacterium Glutamicum ( Crystal Form I) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:As1101

b:23.9
occ:1.00
 AS C:CAC1101 0.0 23.9 1.0
O2 C:CAC1101 1.7 25.2 1.0
O1 C:CAC1101 1.8 20.2 1.0
C2 C:CAC1101 2.0 26.2 1.0
C1 C:CAC1101 2.0 24.0 1.0
ZN C:ZN1092 3.2 22.3 1.0
ZN C:ZN1091 3.2 11.2 1.0
OE1 C:GLU37 3.7 33.4 1.0
O1 C:CAC1095 3.8 19.2 1.0
OE2 H:GLU26 4.0 12.9 1.0
O H:HOH2016 4.0 29.5 1.0
O2 C:CAC1095 4.1 26.0 1.0
O C:HOH2013 4.3 41.5 1.0
NZ C:LYS30 4.3 25.4 1.0
O H:HOH2017 4.4 43.0 1.0
CD H:GLU26 4.5 11.1 1.0
OE1 H:GLU26 4.5 11.4 1.0
AS C:CAC1095 4.6 22.2 1.0
OE2 H:GLU37 4.6 34.5 1.0
O H:GLY82 4.7 14.4 1.0
OE1 H:GLU37 4.7 34.5 1.0
OE2 C:GLU26 4.7 12.3 1.0
O H:LEU83 4.8 14.0 1.0
CD C:GLU37 4.8 31.2 1.0
CA H:LEU83 5.0 13.2 1.0

Reference:

K.Ziegler, R.Benz, G.E.Schulz. A Putative Alpha-Helical Porin From Corynebacterium Glutamicum. J.Mol.Biol. V. 379 482 2008.
ISSN: ISSN 0022-2836
PubMed: 18462756
DOI: 10.1016/J.JMB.2008.04.017
Page generated: Wed Jul 10 11:30:49 2024

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