Zinc in PDB 1kb6: Crystal Structure of Vdr Dna-Binding Domain Bound to Rat Osteocalcin (Oc) Response Element
Protein crystallography data
The structure of Crystal Structure of Vdr Dna-Binding Domain Bound to Rat Osteocalcin (Oc) Response Element, PDB code: 1kb6
was solved by
P.L.Shaffer,
D.T.Gewirth,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
50.00 /
2.70
|
Space group
|
P 43 21 2
|
Cell size a, b, c (Å), α, β, γ (°)
|
61.150,
61.150,
241.800,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
22.3 /
27.5
|
Zinc Binding Sites:
The binding sites of Zinc atom in the Crystal Structure of Vdr Dna-Binding Domain Bound to Rat Osteocalcin (Oc) Response Element
(pdb code 1kb6). 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 Vdr Dna-Binding Domain Bound to Rat Osteocalcin (Oc) Response Element, PDB code: 1kb6:
Jump to Zinc binding site number:
1;
2;
3;
4;
Zinc binding site 1 out
of 4 in 1kb6
Go back to
Zinc Binding Sites List in 1kb6
Zinc binding site 1 out
of 4 in the Crystal Structure of Vdr Dna-Binding Domain Bound to Rat Osteocalcin (Oc) Response Element
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 Vdr Dna-Binding Domain Bound to Rat Osteocalcin (Oc) Response Element within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn150
b:58.0
occ:1.00
|
SG
|
A:CYS24
|
2.2
|
59.0
|
1.0
|
SG
|
A:CYS27
|
2.3
|
57.1
|
1.0
|
SG
|
A:CYS44
|
2.3
|
55.9
|
1.0
|
SG
|
A:CYS41
|
2.4
|
57.2
|
1.0
|
CB
|
A:CYS24
|
3.2
|
61.2
|
1.0
|
CB
|
A:CYS44
|
3.3
|
56.5
|
1.0
|
CB
|
A:CYS27
|
3.4
|
59.1
|
1.0
|
CB
|
A:CYS41
|
3.4
|
57.3
|
1.0
|
N
|
A:CYS27
|
3.5
|
58.7
|
1.0
|
CA
|
A:CYS27
|
4.0
|
60.2
|
1.0
|
NH1
|
A:ARG73
|
4.0
|
70.4
|
1.0
|
N
|
A:CYS41
|
4.0
|
57.8
|
1.0
|
N
|
A:CYS44
|
4.2
|
57.8
|
1.0
|
CB
|
A:VAL26
|
4.2
|
57.2
|
1.0
|
CA
|
A:CYS41
|
4.3
|
58.4
|
1.0
|
CA
|
A:CYS44
|
4.4
|
57.5
|
1.0
|
CB
|
A:ASP29
|
4.5
|
71.8
|
1.0
|
N
|
A:GLY28
|
4.5
|
63.5
|
1.0
|
C
|
A:VAL26
|
4.6
|
57.8
|
1.0
|
C
|
A:CYS27
|
4.6
|
62.0
|
1.0
|
CA
|
A:CYS24
|
4.7
|
61.4
|
1.0
|
N
|
A:ASP29
|
4.7
|
68.6
|
1.0
|
CA
|
A:VAL26
|
4.8
|
57.7
|
1.0
|
N
|
A:VAL26
|
4.8
|
56.3
|
1.0
|
NH2
|
A:ARG80
|
4.8
|
42.2
|
1.0
|
CG1
|
A:VAL26
|
4.8
|
55.7
|
1.0
|
CD
|
A:ARG73
|
5.0
|
67.0
|
1.0
|
C
|
A:CYS41
|
5.0
|
60.1
|
1.0
|
|
Zinc binding site 2 out
of 4 in 1kb6
Go back to
Zinc Binding Sites List in 1kb6
Zinc binding site 2 out
of 4 in the Crystal Structure of Vdr Dna-Binding Domain Bound to Rat Osteocalcin (Oc) Response Element
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 Vdr Dna-Binding Domain Bound to Rat Osteocalcin (Oc) Response Element within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn151
b:57.9
occ:1.00
|
SG
|
A:CYS60
|
2.2
|
59.3
|
1.0
|
SG
|
A:CYS79
|
2.2
|
50.7
|
1.0
|
SG
|
A:CYS76
|
2.3
|
57.8
|
1.0
|
SG
|
A:CYS66
|
2.3
|
57.2
|
1.0
|
CB
|
A:CYS79
|
3.2
|
50.5
|
1.0
|
CB
|
A:CYS66
|
3.4
|
54.5
|
1.0
|
CB
|
A:CYS76
|
3.4
|
61.6
|
1.0
|
CB
|
A:CYS60
|
3.4
|
61.2
|
1.0
|
N
|
A:CYS66
|
4.0
|
53.6
|
1.0
|
CA
|
A:CYS60
|
4.1
|
62.8
|
1.0
|
N
|
A:CYS79
|
4.2
|
51.0
|
1.0
|
CA
|
A:GLY64
|
4.2
|
58.5
|
1.0
|
N
|
A:GLY64
|
4.2
|
60.2
|
1.0
|
CA
|
A:CYS79
|
4.3
|
50.0
|
1.0
|
CA
|
A:CYS66
|
4.3
|
54.7
|
1.0
|
N
|
A:ASP65
|
4.4
|
57.6
|
1.0
|
CD
|
A:PRO61
|
4.7
|
61.1
|
1.0
|
C
|
A:GLY64
|
4.7
|
58.0
|
1.0
|
CA
|
A:CYS76
|
4.8
|
62.5
|
1.0
|
CB
|
A:PHE62
|
4.9
|
64.0
|
1.0
|
CD2
|
A:PHE62
|
5.0
|
65.8
|
1.0
|
CB
|
A:ALA78
|
5.0
|
50.7
|
1.0
|
C
|
A:CYS60
|
5.0
|
62.7
|
1.0
|
|
Zinc binding site 3 out
of 4 in 1kb6
Go back to
Zinc Binding Sites List in 1kb6
Zinc binding site 3 out
of 4 in the Crystal Structure of Vdr Dna-Binding Domain Bound to Rat Osteocalcin (Oc) Response Element
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 Vdr Dna-Binding Domain Bound to Rat Osteocalcin (Oc) Response Element within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Zn350
b:68.6
occ:1.00
|
SG
|
B:CYS227
|
2.2
|
85.3
|
1.0
|
SG
|
B:CYS224
|
2.2
|
82.0
|
1.0
|
SG
|
B:CYS241
|
2.4
|
71.7
|
1.0
|
SG
|
B:CYS244
|
2.4
|
71.0
|
1.0
|
CB
|
B:CYS227
|
2.9
|
83.5
|
1.0
|
CB
|
B:CYS241
|
3.1
|
70.3
|
1.0
|
CB
|
B:CYS224
|
3.2
|
84.5
|
1.0
|
CB
|
B:CYS244
|
3.4
|
67.4
|
1.0
|
N
|
B:CYS227
|
3.5
|
82.5
|
1.0
|
N
|
B:CYS241
|
3.8
|
68.3
|
1.0
|
CA
|
B:CYS227
|
3.8
|
83.1
|
1.0
|
CA
|
B:CYS241
|
4.0
|
70.5
|
1.0
|
NH1
|
B:ARG273
|
4.2
|
79.6
|
1.0
|
N
|
B:CYS244
|
4.2
|
67.7
|
1.0
|
CB
|
B:ASP229
|
4.3
|
84.7
|
1.0
|
CA
|
B:CYS244
|
4.4
|
67.6
|
1.0
|
C
|
B:CYS227
|
4.5
|
82.5
|
1.0
|
CD
|
B:ARG273
|
4.6
|
84.9
|
1.0
|
O
|
B:CYS241
|
4.6
|
72.8
|
1.0
|
C
|
B:VAL226
|
4.7
|
81.8
|
1.0
|
CB
|
B:VAL226
|
4.7
|
80.7
|
1.0
|
N
|
B:GLY228
|
4.7
|
82.0
|
1.0
|
C
|
B:CYS241
|
4.7
|
71.4
|
1.0
|
CA
|
B:CYS224
|
4.7
|
85.5
|
1.0
|
N
|
B:ASP229
|
4.8
|
83.2
|
1.0
|
C
|
B:THR240
|
4.9
|
66.7
|
1.0
|
N
|
B:VAL226
|
5.0
|
81.8
|
1.0
|
CZ
|
B:ARG273
|
5.0
|
81.0
|
1.0
|
|
Zinc binding site 4 out
of 4 in 1kb6
Go back to
Zinc Binding Sites List in 1kb6
Zinc binding site 4 out
of 4 in the Crystal Structure of Vdr Dna-Binding Domain Bound to Rat Osteocalcin (Oc) Response Element
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 Vdr Dna-Binding Domain Bound to Rat Osteocalcin (Oc) Response Element within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Zn351
b:80.5
occ:1.00
|
SG
|
B:CYS260
|
2.3
|
81.7
|
1.0
|
SG
|
B:CYS276
|
2.4
|
77.6
|
1.0
|
SG
|
B:CYS279
|
2.4
|
77.8
|
1.0
|
SG
|
B:CYS266
|
2.4
|
79.7
|
1.0
|
CB
|
B:CYS260
|
3.2
|
81.0
|
1.0
|
CB
|
B:CYS279
|
3.3
|
74.8
|
1.0
|
CB
|
B:CYS276
|
3.4
|
81.7
|
1.0
|
CB
|
B:CYS266
|
3.4
|
82.7
|
1.0
|
CA
|
B:CYS260
|
4.1
|
82.0
|
1.0
|
N
|
B:CYS266
|
4.2
|
86.0
|
1.0
|
N
|
B:CYS279
|
4.2
|
73.4
|
1.0
|
CD1
|
B:PHE262
|
4.3
|
89.7
|
1.0
|
CA
|
B:CYS279
|
4.4
|
73.2
|
1.0
|
CA
|
B:CYS266
|
4.4
|
84.9
|
1.0
|
N
|
B:GLY264
|
4.5
|
91.1
|
1.0
|
CA
|
B:GLY264
|
4.6
|
89.9
|
1.0
|
CD
|
B:PRO261
|
4.7
|
86.5
|
1.0
|
C
|
B:CYS260
|
4.7
|
84.2
|
1.0
|
CB
|
B:PHE262
|
4.8
|
89.3
|
1.0
|
N
|
B:PRO261
|
4.8
|
86.3
|
1.0
|
N
|
B:PHE262
|
4.8
|
88.5
|
1.0
|
N
|
B:ASP265
|
4.8
|
88.8
|
1.0
|
CA
|
B:CYS276
|
4.9
|
82.9
|
1.0
|
CG
|
B:PHE262
|
5.0
|
89.4
|
1.0
|
C
|
B:GLY264
|
5.0
|
89.0
|
1.0
|
|
Reference:
P.L.Shaffer,
D.T.Gewirth.
Structural Basis of Vdr-Dna Interactions on Direct Repeat Response Elements. Embo J. V. 21 2242 2002.
ISSN: ISSN 0261-4189
PubMed: 11980721
DOI: 10.1093/EMBOJ/21.9.2242
Page generated: Sun Oct 13 04:15:38 2024
|