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
Go back to
Zinc Binding Sites List in 2w57
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: Thu Oct 17 04:44:12 2024
|