Zinc in PDB 2o5i: Crystal Structure of the T. Thermophilus Rna Polymerase Elongation Complex
Enzymatic activity of Crystal Structure of the T. Thermophilus Rna Polymerase Elongation Complex
All present enzymatic activity of Crystal Structure of the T. Thermophilus Rna Polymerase Elongation Complex:
2.7.7.6;
Protein crystallography data
The structure of Crystal Structure of the T. Thermophilus Rna Polymerase Elongation Complex, PDB code: 2o5i
was solved by
D.G.Vassylyev,
T.H.Tahirov,
M.N.Vassylyeva,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
20.00 /
2.50
|
Space group
|
P 41
|
Cell size a, b, c (Å), α, β, γ (°)
|
156.211,
156.211,
499.229,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
23.8 /
26.7
|
Other elements in 2o5i:
The structure of Crystal Structure of the T. Thermophilus Rna Polymerase Elongation Complex also contains other interesting chemical elements:
Zinc Binding Sites:
The binding sites of Zinc atom in the Crystal Structure of the T. Thermophilus Rna Polymerase Elongation Complex
(pdb code 2o5i). 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 T. Thermophilus Rna Polymerase Elongation Complex, PDB code: 2o5i:
Jump to Zinc binding site number:
1;
2;
3;
4;
Zinc binding site 1 out
of 4 in 2o5i
Go back to
Zinc Binding Sites List in 2o5i
Zinc binding site 1 out
of 4 in the Crystal Structure of the T. Thermophilus Rna Polymerase Elongation Complex
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 T. Thermophilus Rna Polymerase Elongation Complex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Zn4058
b:82.8
occ:1.00
|
SG
|
D:CYS76
|
2.3
|
78.4
|
1.0
|
SG
|
D:CYS60
|
2.4
|
79.1
|
1.0
|
SG
|
D:CYS73
|
2.5
|
78.8
|
1.0
|
SG
|
D:CYS58
|
2.5
|
82.0
|
1.0
|
CB
|
D:CYS76
|
3.4
|
73.6
|
1.0
|
CB
|
D:CYS73
|
3.4
|
78.1
|
1.0
|
CB
|
D:ALA59
|
3.6
|
78.3
|
1.0
|
N
|
D:CYS60
|
3.7
|
79.2
|
1.0
|
CB
|
D:CYS58
|
3.9
|
81.7
|
1.0
|
CB
|
D:CYS60
|
3.9
|
79.5
|
1.0
|
N
|
D:GLY61
|
4.1
|
79.4
|
1.0
|
N
|
D:ALA59
|
4.2
|
80.4
|
1.0
|
N
|
D:LYS62
|
4.3
|
81.4
|
1.0
|
CA
|
D:CYS60
|
4.3
|
79.2
|
1.0
|
O
|
D:CYS76
|
4.3
|
72.1
|
1.0
|
CA
|
D:ALA59
|
4.4
|
78.8
|
1.0
|
CB
|
D:LYS62
|
4.4
|
81.4
|
1.0
|
CA
|
D:CYS76
|
4.4
|
71.2
|
1.0
|
CG
|
D:LYS62
|
4.4
|
79.9
|
1.0
|
N
|
D:CYS76
|
4.5
|
71.8
|
1.0
|
CG2
|
D:VAL78
|
4.5
|
71.1
|
1.0
|
C
|
D:ALA59
|
4.6
|
78.8
|
1.0
|
C
|
D:CYS60
|
4.7
|
79.1
|
1.0
|
C
|
D:CYS76
|
4.7
|
71.6
|
1.0
|
CA
|
D:CYS73
|
5.0
|
77.8
|
1.0
|
CA
|
D:LYS62
|
5.0
|
83.0
|
1.0
|
|
Zinc binding site 2 out
of 4 in 2o5i
Go back to
Zinc Binding Sites List in 2o5i
Zinc binding site 2 out
of 4 in the Crystal Structure of the T. Thermophilus Rna Polymerase Elongation Complex
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 T. Thermophilus Rna Polymerase Elongation Complex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Zn6112
b:65.8
occ:1.00
|
SG
|
D:CYS1112
|
2.3
|
68.0
|
1.0
|
SG
|
D:CYS1201
|
2.3
|
63.7
|
1.0
|
SG
|
D:CYS1194
|
2.3
|
64.6
|
1.0
|
SG
|
D:CYS1204
|
2.3
|
63.2
|
1.0
|
CB
|
D:CYS1204
|
3.2
|
59.8
|
1.0
|
CB
|
D:CYS1112
|
3.4
|
67.5
|
1.0
|
CB
|
D:CYS1194
|
3.4
|
62.7
|
1.0
|
CB
|
D:CYS1201
|
3.6
|
65.5
|
1.0
|
CA
|
D:CYS1194
|
3.7
|
61.3
|
1.0
|
N
|
D:CYS1201
|
3.8
|
67.6
|
1.0
|
N
|
D:GLN1195
|
4.2
|
62.9
|
1.0
|
CA
|
D:CYS1201
|
4.3
|
66.2
|
1.0
|
CA
|
D:CYS1204
|
4.4
|
61.1
|
1.0
|
C
|
D:CYS1194
|
4.5
|
61.8
|
1.0
|
N
|
D:CYS1204
|
4.6
|
63.9
|
1.0
|
CA
|
D:CYS1112
|
4.6
|
69.6
|
1.0
|
N
|
D:CYS1112
|
4.7
|
71.0
|
1.0
|
N
|
D:CYS1194
|
4.9
|
60.5
|
1.0
|
C
|
D:VAL1200
|
4.9
|
68.5
|
1.0
|
O
|
D:CYS1112
|
4.9
|
69.3
|
1.0
|
C
|
D:CYS1201
|
5.0
|
67.0
|
1.0
|
OG1
|
D:THR1196
|
5.0
|
70.7
|
1.0
|
|
Zinc binding site 3 out
of 4 in 2o5i
Go back to
Zinc Binding Sites List in 2o5i
Zinc binding site 3 out
of 4 in the Crystal Structure of the T. Thermophilus Rna Polymerase Elongation Complex
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 T. Thermophilus Rna Polymerase Elongation Complex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
N:Zn5058
b:71.5
occ:1.00
|
SG
|
N:CYS76
|
2.3
|
75.7
|
1.0
|
SG
|
N:CYS60
|
2.3
|
72.5
|
1.0
|
SG
|
N:CYS58
|
2.4
|
72.0
|
1.0
|
SG
|
N:CYS73
|
2.5
|
76.4
|
1.0
|
CB
|
N:CYS76
|
3.3
|
76.6
|
1.0
|
OG
|
D:SER1300
|
3.4
|
90.7
|
1.0
|
N
|
N:CYS60
|
3.5
|
66.2
|
1.0
|
CB
|
N:CYS73
|
3.6
|
75.7
|
1.0
|
CB
|
N:ALA59
|
3.6
|
68.2
|
1.0
|
CB
|
N:CYS60
|
3.8
|
69.0
|
1.0
|
CB
|
N:CYS58
|
3.9
|
70.1
|
1.0
|
N
|
N:GLY61
|
4.1
|
71.0
|
1.0
|
N
|
N:ALA59
|
4.1
|
66.8
|
1.0
|
CA
|
N:CYS60
|
4.2
|
68.1
|
1.0
|
CA
|
N:ALA59
|
4.3
|
67.3
|
1.0
|
N
|
N:LYS62
|
4.3
|
74.0
|
1.0
|
O
|
N:CYS76
|
4.4
|
78.7
|
1.0
|
CA
|
N:CYS76
|
4.4
|
77.7
|
1.0
|
C
|
N:ALA59
|
4.5
|
66.7
|
1.0
|
CB
|
D:SER1300
|
4.5
|
91.8
|
1.0
|
CB
|
N:LYS62
|
4.5
|
72.3
|
1.0
|
N
|
N:CYS76
|
4.6
|
77.1
|
1.0
|
C
|
N:CYS60
|
4.6
|
69.6
|
1.0
|
CE2
|
D:PHE1293
|
4.7
|
90.4
|
1.0
|
CG2
|
N:VAL78
|
4.7
|
73.5
|
1.0
|
C
|
N:CYS76
|
4.7
|
78.7
|
1.0
|
CG
|
N:LYS62
|
4.7
|
70.5
|
1.0
|
CD2
|
D:PHE1293
|
4.9
|
91.0
|
1.0
|
|
Zinc binding site 4 out
of 4 in 2o5i
Go back to
Zinc Binding Sites List in 2o5i
Zinc binding site 4 out
of 4 in the Crystal Structure of the T. Thermophilus Rna Polymerase Elongation Complex
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 T. Thermophilus Rna Polymerase Elongation Complex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
N:Zn7112
b:73.9
occ:1.00
|
SG
|
N:CYS1194
|
2.3
|
72.1
|
1.0
|
SG
|
N:CYS1112
|
2.4
|
74.8
|
1.0
|
SG
|
N:CYS1204
|
2.4
|
69.8
|
1.0
|
SG
|
N:CYS1201
|
2.4
|
71.2
|
1.0
|
CB
|
N:CYS1112
|
3.3
|
76.6
|
1.0
|
CB
|
N:CYS1204
|
3.3
|
63.9
|
1.0
|
CB
|
N:CYS1194
|
3.4
|
76.9
|
1.0
|
CB
|
N:CYS1201
|
3.7
|
65.0
|
1.0
|
CA
|
N:CYS1194
|
3.7
|
78.7
|
1.0
|
N
|
N:CYS1201
|
4.0
|
63.4
|
1.0
|
N
|
N:GLN1195
|
4.2
|
80.2
|
1.0
|
NH1
|
N:ARG1189
|
4.3
|
87.5
|
1.0
|
CA
|
N:CYS1201
|
4.4
|
62.6
|
1.0
|
OG1
|
N:THR1196
|
4.5
|
81.2
|
1.0
|
CA
|
N:CYS1204
|
4.5
|
61.9
|
1.0
|
CA
|
N:CYS1112
|
4.5
|
77.6
|
1.0
|
C
|
N:CYS1194
|
4.5
|
79.7
|
1.0
|
N
|
N:CYS1204
|
4.6
|
62.5
|
1.0
|
N
|
N:CYS1112
|
4.6
|
78.6
|
1.0
|
O
|
N:CYS1112
|
4.8
|
77.8
|
1.0
|
N
|
N:CYS1194
|
4.9
|
78.9
|
1.0
|
CZ
|
N:ARG1189
|
5.0
|
87.3
|
1.0
|
O
|
N:HOH8129
|
5.0
|
41.8
|
1.0
|
|
Reference:
D.G.Vassylyev,
M.N.Vassylyeva,
A.Perederina,
T.H.Tahirov,
I.Artsimovitch.
Structural Basis For Transcription Elongation By Bacterial Rna Polymerase. Nature V. 448 157 2007.
ISSN: ISSN 0028-0836
PubMed: 17581590
DOI: 10.1038/NATURE05932
Page generated: Thu Oct 17 02:27:58 2024
|