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Zinc in PDB 2w57: Crystal Structure of the Vibrio Cholerae Ferric Uptake Regulator (Fur) Reveals Structural Rearrangement of the Dna-Binding Domains

Protein crystallography data

The structure of Crystal Structure of the Vibrio Cholerae Ferric Uptake Regulator (Fur) Reveals Structural Rearrangement of the Dna-Binding Domains, PDB code: 2w57 was solved by M.A.Sheikh, G.L.Taylor, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 62.87 / 2.60
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 88.880, 88.880, 85.070, 90.00, 90.00, 90.00
R / Rfree (%) 21.6 / 25.9

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of the Vibrio Cholerae Ferric Uptake Regulator (Fur) Reveals Structural Rearrangement of the Dna-Binding Domains (pdb code 2w57). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Crystal Structure of the Vibrio Cholerae Ferric Uptake Regulator (Fur) Reveals Structural Rearrangement of the Dna-Binding Domains, PDB code: 2w57:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 2w57

Go back to Zinc Binding Sites List in 2w57
Zinc binding site 1 out of 4 in the Crystal Structure of the Vibrio Cholerae Ferric Uptake Regulator (Fur) Reveals Structural Rearrangement of the Dna-Binding Domains


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of the Vibrio Cholerae Ferric Uptake Regulator (Fur) Reveals Structural Rearrangement of the Dna-Binding Domains within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn201

b:40.8
occ:1.00
OD2 A:ASP89 2.0 32.0 1.0
OE2 A:GLU108 2.1 36.3 1.0
NE2 A:HIS125 2.2 35.0 1.0
NE2 A:HIS87 2.3 39.1 1.0
CG A:ASP89 2.7 33.1 1.0
OD1 A:ASP89 2.7 33.1 1.0
CD A:GLU108 3.0 36.4 1.0
CE1 A:HIS125 3.0 34.7 1.0
CE1 A:HIS87 3.2 38.7 1.0
OE1 A:GLU108 3.2 37.0 1.0
CD2 A:HIS125 3.3 34.6 1.0
CD2 A:HIS87 3.3 37.6 1.0
O A:HOH2042 3.5 44.4 1.0
CB A:ASP89 4.1 33.5 1.0
ND1 A:HIS125 4.2 35.5 1.0
ND1 A:HIS87 4.3 38.3 1.0
CG A:HIS125 4.4 35.3 1.0
CG A:GLU108 4.4 35.5 1.0
CG A:HIS87 4.4 37.9 1.0
OE1 A:GLN111 4.5 37.5 1.0
NE2 A:GLN111 4.5 35.8 1.0
N A:ASP89 4.8 34.4 1.0
C A:HIS88 4.8 35.2 1.0
O A:HIS88 4.9 34.9 1.0
CA A:ASP89 4.9 33.8 1.0
CD A:GLN111 4.9 36.4 1.0

Zinc binding site 2 out of 4 in 2w57

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Zinc binding site 2 out of 4 in the Crystal Structure of the Vibrio Cholerae Ferric Uptake Regulator (Fur) Reveals Structural Rearrangement of the Dna-Binding Domains


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of the Vibrio Cholerae Ferric Uptake Regulator (Fur) Reveals Structural Rearrangement of the Dna-Binding Domains within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn202

b:43.5
occ:1.00
OE2 A:GLU81 2.1 25.8 1.0
NE2 A:HIS88 2.1 35.7 1.0
NE2 A:HIS33 2.1 26.5 1.0
NE2 A:HIS90 2.4 33.4 1.0
CD A:GLU81 2.6 27.3 1.0
OE1 A:GLU81 2.7 30.8 1.0
CD2 A:HIS88 2.9 35.6 1.0
CD2 A:HIS90 3.0 32.8 1.0
CE1 A:HIS33 3.1 27.0 1.0
CE1 A:HIS88 3.1 35.3 1.0
CD2 A:HIS33 3.1 26.7 1.0
CE1 A:HIS90 3.5 33.7 1.0
OE2 A:GLU101 3.9 40.2 1.0
CG A:GLU81 4.0 26.6 1.0
O A:HOH2035 4.0 42.2 1.0
CG A:HIS88 4.1 35.4 1.0
NE2 A:HIS71 4.1 33.6 1.0
ND1 A:HIS88 4.1 35.8 1.0
ND1 A:HIS33 4.2 26.2 1.0
CG A:HIS33 4.2 27.7 1.0
CG A:HIS90 4.3 32.7 1.0
ND1 A:HIS90 4.5 32.5 1.0
CD A:GLU101 4.5 39.1 1.0
CG A:GLU101 4.6 37.7 1.0
CD2 A:HIS71 4.6 31.2 1.0
CB A:GLU81 4.6 26.1 1.0
CE1 A:HIS71 4.9 33.4 1.0

Zinc binding site 3 out of 4 in 2w57

Go back to Zinc Binding Sites List in 2w57
Zinc binding site 3 out of 4 in the Crystal Structure of the Vibrio Cholerae Ferric Uptake Regulator (Fur) Reveals Structural Rearrangement of the Dna-Binding Domains


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of the Vibrio Cholerae Ferric Uptake Regulator (Fur) Reveals Structural Rearrangement of the Dna-Binding Domains within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn201

b:27.9
occ:1.00
OD2 B:ASP89 1.9 23.6 1.0
NE2 B:HIS87 2.1 21.6 1.0
OE2 B:GLU108 2.1 26.2 1.0
NE2 B:HIS125 2.2 25.3 1.0
CE1 B:HIS87 2.7 22.2 1.0
CG B:ASP89 2.8 22.9 1.0
CD B:GLU108 2.8 26.9 1.0
OE1 B:GLU108 2.9 25.2 1.0
OD1 B:ASP89 3.0 22.7 1.0
CD2 B:HIS125 3.1 25.9 1.0
CE1 B:HIS125 3.2 26.0 1.0
CD2 B:HIS87 3.3 20.7 1.0
ND1 B:HIS87 4.0 21.0 1.0
O B:HOH2034 4.0 24.0 1.0
CB B:ASP89 4.2 21.6 1.0
CG B:HIS125 4.3 27.8 1.0
OE1 B:GLN111 4.3 29.4 1.0
ND1 B:HIS125 4.3 27.7 1.0
CG B:HIS87 4.3 20.4 1.0
CG B:GLU108 4.3 27.2 1.0
NE2 B:GLN111 4.7 26.7 1.0
CD B:GLN111 4.9 29.9 1.0
O B:HOH2031 5.0 36.2 1.0

Zinc binding site 4 out of 4 in 2w57

Go back to Zinc Binding Sites List in 2w57
Zinc binding site 4 out of 4 in the Crystal Structure of the Vibrio Cholerae Ferric Uptake Regulator (Fur) Reveals Structural Rearrangement of the Dna-Binding Domains


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of the Vibrio Cholerae Ferric Uptake Regulator (Fur) Reveals Structural Rearrangement of the Dna-Binding Domains within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn202

b:32.1
occ:1.00
NE2 B:HIS33 2.0 22.7 1.0
OE2 B:GLU81 2.1 27.3 1.0
NE2 B:HIS88 2.1 17.7 1.0
NE2 B:HIS90 2.2 20.3 1.0
CD B:GLU81 2.6 23.7 1.0
OE1 B:GLU81 2.7 25.4 1.0
CD2 B:HIS33 3.0 23.2 1.0
CE1 B:HIS88 3.0 18.0 1.0
CE1 B:HIS33 3.1 24.1 1.0
CD2 B:HIS88 3.1 16.6 1.0
CD2 B:HIS90 3.1 20.8 1.0
CE1 B:HIS90 3.2 20.1 1.0
NE2 B:HIS71 3.7 34.4 1.0
O B:HOH2025 3.8 23.4 1.0
CG B:GLU81 4.0 23.6 1.0
ND1 B:HIS88 4.1 18.7 1.0
ND1 B:HIS33 4.1 25.4 1.0
CG B:HIS33 4.2 24.7 1.0
CG B:HIS88 4.2 18.9 1.0
ND1 B:HIS90 4.3 19.6 1.0
CG B:HIS90 4.3 22.1 1.0
CE1 B:HIS71 4.4 35.2 1.0
CD2 B:HIS71 4.5 32.5 1.0
CB B:GLU81 4.7 22.3 1.0
OE2 B:GLU101 4.7 27.0 1.0

Reference:

M.A.Sheikh, G.L.Taylor. Crystal Structure of the Vibrio Cholerae Ferric Uptake Regulator (Fur) Reveals Insights Into Metal Co-Ordination. Mol.Microbiol. V. 72 1208 2009.
ISSN: ISSN 0950-382X
PubMed: 19400801
DOI: 10.1111/J.1365-2958.2009.06718.X
Page generated: Wed Dec 16 03:56:57 2020

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