Zinc in PDB 4ayb: Rnap at 3.2ANG
Enzymatic activity of Rnap at 3.2ANG
All present enzymatic activity of Rnap at 3.2ANG:
2.7.7.6;
Protein crystallography data
The structure of Rnap at 3.2ANG, PDB code: 4ayb
was solved by
M.N.Wojtas,
M.Mogni,
O.Millet,
S.D.Bell,
N.G.A.Abrescia,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
|
Resolution Low / High (Å)
|
40.10 /
3.20
|
|
Space group
|
P 21 21 2
|
|
Cell size a, b, c (Å), α, β, γ (°)
|
195.725,
212.415,
128.757,
90.00,
90.00,
90.00
|
|
R / Rfree (%)
|
24.3 /
30.1
|
Other elements in 4ayb:
The structure of Rnap at 3.2ANG also contains other interesting chemical elements:
Zinc Binding Sites:
The binding sites of Zinc atom in the Rnap at 3.2ANG
(pdb code 4ayb). This binding sites where shown within
5.0 Angstroms radius around Zinc atom.
In total 10 binding sites of Zinc where determined in the
Rnap at 3.2ANG, PDB code: 4ayb:
Jump to Zinc binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
9;
10;
Zinc binding site 1 out
of 10 in 4ayb
Go back to
Zinc Binding Sites List in 4ayb
Zinc binding site 1 out
of 10 in the Rnap at 3.2ANG
 Mono view
 Stereo pair view
|
|
A full contact list of Zinc with other atoms in the Zn binding
site number 1 of Rnap at 3.2ANG within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn1880
b:81.4
occ:1.00
|
HD2
|
A:HIS71
|
2.0
|
81.4
|
1.0
|
|
NE2
|
A:HIS71
|
2.1
|
98.3
|
1.0
|
|
SG
|
A:CYS68
|
2.1
|
0.7
|
1.0
|
|
SG
|
A:CYS58
|
2.2
|
0.3
|
1.0
|
|
SG
|
A:CYS61
|
2.3
|
0.9
|
1.0
|
|
CD2
|
A:HIS71
|
2.3
|
97.6
|
1.0
|
|
HA
|
A:CYS68
|
2.7
|
81.4
|
1.0
|
|
HB2
|
A:CYS61
|
2.8
|
81.4
|
1.0
|
|
CB
|
A:CYS68
|
2.8
|
0.6
|
1.0
|
|
HB3
|
A:CYS68
|
3.0
|
81.4
|
1.0
|
|
CA
|
A:CYS68
|
3.0
|
0.9
|
1.0
|
|
CB
|
A:CYS61
|
3.1
|
0.1
|
1.0
|
|
C
|
A:CYS68
|
3.2
|
0.3
|
1.0
|
|
HA2
|
A:GLY50
|
3.3
|
81.4
|
1.0
|
|
O
|
A:CYS68
|
3.3
|
0.2
|
1.0
|
|
CE1
|
A:HIS71
|
3.4
|
97.4
|
1.0
|
|
CB
|
A:CYS58
|
3.5
|
0.5
|
1.0
|
|
HB3
|
A:CYS58
|
3.6
|
81.4
|
1.0
|
|
HB2
|
A:CYS58
|
3.6
|
81.4
|
1.0
|
|
HB3
|
A:CYS61
|
3.6
|
81.4
|
1.0
|
|
CG
|
A:HIS71
|
3.6
|
96.2
|
1.0
|
|
HD2
|
A:PRO69
|
3.7
|
81.4
|
1.0
|
|
HB2
|
A:CYS68
|
3.7
|
81.4
|
1.0
|
|
HE1
|
A:HIS71
|
3.9
|
81.4
|
1.0
|
|
N
|
A:PRO69
|
3.9
|
86.1
|
1.0
|
|
ND1
|
A:HIS71
|
4.1
|
96.1
|
1.0
|
|
CA
|
A:GLY50
|
4.2
|
84.4
|
1.0
|
|
CD
|
A:PRO69
|
4.3
|
0.5
|
1.0
|
|
CA
|
A:CYS61
|
4.3
|
0.3
|
1.0
|
|
OG1
|
A:THR60
|
4.4
|
0.9
|
1.0
|
|
H
|
A:CYS61
|
4.4
|
81.4
|
1.0
|
|
N
|
A:CYS61
|
4.4
|
0.0
|
1.0
|
|
N
|
A:CYS68
|
4.5
|
0.1
|
1.0
|
|
O
|
A:GLY70
|
4.5
|
81.0
|
1.0
|
|
HG21
|
A:VAL51
|
4.5
|
81.4
|
1.0
|
|
HA3
|
A:GLY50
|
4.5
|
81.4
|
1.0
|
|
HG1
|
A:THR60
|
4.6
|
81.4
|
1.0
|
|
O
|
A:PRO69
|
4.7
|
82.2
|
1.0
|
|
HB2
|
A:HIS71
|
4.7
|
81.4
|
1.0
|
|
H
|
A:GLY50
|
4.7
|
81.4
|
1.0
|
|
H
|
A:GLY62
|
4.7
|
81.4
|
1.0
|
|
N
|
A:GLY50
|
4.8
|
84.9
|
1.0
|
|
HD3
|
A:PRO69
|
4.8
|
81.4
|
1.0
|
|
CB
|
A:HIS71
|
4.8
|
95.2
|
1.0
|
|
H
|
A:VAL51
|
4.8
|
81.4
|
1.0
|
|
C
|
A:PRO69
|
4.8
|
82.0
|
1.0
|
|
CA
|
A:CYS58
|
4.9
|
0.3
|
1.0
|
|
HB2
|
A:ASN63
|
4.9
|
81.4
|
1.0
|
|
HA
|
A:CYS61
|
4.9
|
81.4
|
1.0
|
|
C
|
A:THR60
|
4.9
|
0.8
|
1.0
|
|
H
|
A:CYS68
|
4.9
|
81.4
|
1.0
|
|
HD1
|
A:HIS71
|
4.9
|
81.4
|
1.0
|
|
H
|
A:THR60
|
4.9
|
81.4
|
1.0
|
|
O
|
A:ASN67
|
5.0
|
0.7
|
1.0
|
|
CA
|
A:PRO69
|
5.0
|
82.8
|
1.0
|
|
Zinc binding site 2 out
of 10 in 4ayb
Go back to
Zinc Binding Sites List in 4ayb
Zinc binding site 2 out
of 10 in the Rnap at 3.2ANG
 Mono view
 Stereo pair view
|
|
A full contact list of Zinc with other atoms in the Zn binding
site number 2 of Rnap at 3.2ANG within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn1881
b:81.4
occ:1.00
|
HB3
|
A:CYS149
|
1.6
|
81.4
|
1.0
|
|
HB2
|
A:CYS149
|
1.7
|
81.4
|
1.0
|
|
CB
|
A:CYS149
|
1.8
|
97.2
|
1.0
|
|
HB3
|
A:CYS146
|
1.8
|
81.4
|
1.0
|
|
SG
|
A:CYS98
|
2.1
|
0.4
|
1.0
|
|
SG
|
A:CYS149
|
2.2
|
91.9
|
1.0
|
|
SG
|
A:CYS101
|
2.2
|
0.1
|
1.0
|
|
SG
|
A:CYS146
|
2.3
|
0.8
|
1.0
|
|
CB
|
A:CYS146
|
2.4
|
0.4
|
1.0
|
|
HB2
|
A:CYS146
|
2.9
|
81.4
|
1.0
|
|
CB
|
A:CYS101
|
3.2
|
0.9
|
1.0
|
|
HB3
|
A:CYS101
|
3.3
|
81.4
|
1.0
|
|
HZ
|
A:PHE154
|
3.3
|
81.4
|
1.0
|
|
CA
|
A:CYS149
|
3.3
|
0.2
|
1.0
|
|
HB2
|
A:CYS101
|
3.3
|
81.4
|
1.0
|
|
HG2
|
A:LYS152
|
3.4
|
81.4
|
1.0
|
|
HA
|
A:CYS98
|
3.5
|
81.4
|
1.0
|
|
O
|
A:CYS98
|
3.5
|
94.1
|
1.0
|
|
CB
|
A:CYS98
|
3.5
|
0.2
|
1.0
|
|
O
|
A:CYS149
|
3.7
|
0.5
|
1.0
|
|
HA
|
A:CYS149
|
3.7
|
81.4
|
1.0
|
|
CA
|
A:CYS146
|
3.7
|
0.7
|
1.0
|
|
HA
|
A:CYS146
|
3.8
|
81.4
|
1.0
|
|
HB2
|
A:CYS98
|
3.9
|
81.4
|
1.0
|
|
H
|
A:LYS152
|
3.9
|
81.4
|
1.0
|
|
C
|
A:CYS149
|
3.9
|
0.6
|
1.0
|
|
CA
|
A:CYS98
|
3.9
|
88.1
|
1.0
|
|
CZ
|
A:PHE154
|
4.1
|
0.0
|
1.0
|
|
HG3
|
A:LYS152
|
4.1
|
81.4
|
1.0
|
|
N
|
A:CYS149
|
4.1
|
0.6
|
1.0
|
|
HE2
|
A:LYS152
|
4.1
|
81.4
|
1.0
|
|
CG
|
A:LYS152
|
4.1
|
1.0
|
1.0
|
|
O
|
A:PRO147
|
4.2
|
0.3
|
1.0
|
|
C
|
A:CYS98
|
4.2
|
90.5
|
1.0
|
|
HB3
|
A:CYS98
|
4.3
|
81.4
|
1.0
|
|
C
|
A:CYS146
|
4.4
|
0.9
|
1.0
|
|
C
|
A:HIS148
|
4.4
|
0.8
|
1.0
|
|
O
|
A:HIS148
|
4.5
|
0.2
|
1.0
|
|
HE2
|
A:PHE154
|
4.5
|
81.4
|
1.0
|
|
H
|
A:CYS149
|
4.6
|
81.4
|
1.0
|
|
H
|
A:CYS101
|
4.6
|
81.4
|
1.0
|
|
CA
|
A:CYS101
|
4.7
|
0.1
|
1.0
|
|
H
|
A:GLU151
|
4.7
|
81.4
|
1.0
|
|
CE2
|
A:PHE154
|
4.7
|
0.5
|
1.0
|
|
N
|
A:LYS152
|
4.8
|
0.5
|
1.0
|
|
N
|
A:CYS146
|
4.8
|
0.4
|
1.0
|
|
O
|
A:CYS146
|
4.8
|
0.8
|
1.0
|
|
H
|
A:CYS146
|
4.8
|
81.4
|
1.0
|
|
HG12
|
A:ILE106
|
4.8
|
81.4
|
1.0
|
|
HA
|
A:GLU151
|
4.9
|
81.4
|
1.0
|
|
HE1
|
A:PHE154
|
4.9
|
81.4
|
1.0
|
|
HB2
|
A:LYS152
|
4.9
|
81.4
|
1.0
|
|
CE
|
A:LYS152
|
4.9
|
0.1
|
1.0
|
|
CE1
|
A:PHE154
|
4.9
|
0.8
|
1.0
|
|
HB
|
A:VAL104
|
4.9
|
81.4
|
1.0
|
|
HA
|
A:CYS101
|
5.0
|
81.4
|
1.0
|
|
HB2
|
A:HIS148
|
5.0
|
81.4
|
1.0
|
|
Zinc binding site 3 out
of 10 in 4ayb
Go back to
Zinc Binding Sites List in 4ayb
Zinc binding site 3 out
of 10 in the Rnap at 3.2ANG
 Mono view
 Stereo pair view
|
|
A full contact list of Zinc with other atoms in the Zn binding
site number 3 of Rnap at 3.2ANG within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn1882
b:81.4
occ:1.00
|
OE1
|
C:GLU80
|
2.0
|
66.7
|
1.0
|
|
OE2
|
C:GLU80
|
2.0
|
67.4
|
1.0
|
|
ND1
|
A:HIS426
|
2.0
|
35.5
|
1.0
|
|
CD
|
C:GLU80
|
2.3
|
67.4
|
1.0
|
|
HG1
|
A:THR488
|
2.8
|
81.4
|
1.0
|
|
CE1
|
A:HIS426
|
2.8
|
35.0
|
1.0
|
|
HE1
|
A:HIS426
|
2.9
|
81.4
|
1.0
|
|
HB2
|
A:ARG490
|
2.9
|
81.4
|
1.0
|
|
CG
|
A:HIS426
|
3.1
|
35.4
|
1.0
|
|
OG1
|
A:THR488
|
3.2
|
0.3
|
1.0
|
|
HE
|
A:ARG490
|
3.2
|
81.4
|
1.0
|
|
HB3
|
A:HIS426
|
3.4
|
81.4
|
1.0
|
|
HB2
|
A:HIS426
|
3.6
|
81.4
|
1.0
|
|
CB
|
A:HIS426
|
3.6
|
36.0
|
1.0
|
|
HG3
|
A:ARG490
|
3.8
|
81.4
|
1.0
|
|
CG
|
C:GLU80
|
3.8
|
68.5
|
1.0
|
|
CB
|
A:ARG490
|
3.8
|
54.6
|
1.0
|
|
NE2
|
A:HIS426
|
4.0
|
34.6
|
1.0
|
|
H
|
A:ARG490
|
4.0
|
81.4
|
1.0
|
|
NE
|
A:ARG490
|
4.1
|
54.0
|
1.0
|
|
HB3
|
A:ARG490
|
4.1
|
81.4
|
1.0
|
|
CD2
|
A:HIS426
|
4.2
|
34.9
|
1.0
|
|
HH21
|
A:ARG490
|
4.2
|
81.4
|
1.0
|
|
HD2
|
A:PRO489
|
4.2
|
81.4
|
1.0
|
|
HG3
|
C:GLU80
|
4.2
|
81.4
|
1.0
|
|
HG2
|
C:GLU80
|
4.2
|
81.4
|
1.0
|
|
CG
|
A:ARG490
|
4.3
|
54.9
|
1.0
|
|
HD13
|
A:ILE495
|
4.5
|
81.4
|
1.0
|
|
HB2
|
C:GLU80
|
4.5
|
81.4
|
1.0
|
|
CB
|
A:THR488
|
4.6
|
0.6
|
1.0
|
|
CB
|
C:GLU80
|
4.7
|
68.6
|
1.0
|
|
HA
|
C:SER77
|
4.7
|
81.4
|
1.0
|
|
HB
|
A:THR488
|
4.7
|
81.4
|
1.0
|
|
N
|
A:ARG490
|
4.7
|
31.7
|
1.0
|
|
HB3
|
C:GLU80
|
4.7
|
81.4
|
1.0
|
|
HE2
|
A:HIS426
|
4.7
|
81.4
|
1.0
|
|
CD
|
A:ARG490
|
4.8
|
55.0
|
1.0
|
|
NH2
|
A:ARG490
|
4.8
|
53.2
|
1.0
|
|
HG13
|
A:ILE428
|
4.9
|
81.4
|
1.0
|
|
CA
|
A:ARG490
|
4.9
|
32.3
|
1.0
|
|
HB
|
A:ILE428
|
4.9
|
81.4
|
1.0
|
|
HG12
|
A:ILE428
|
4.9
|
81.4
|
1.0
|
|
CZ
|
A:ARG490
|
5.0
|
54.0
|
1.0
|
|
HG22
|
A:THR488
|
5.0
|
81.4
|
1.0
|
|
Zinc binding site 4 out
of 10 in 4ayb
Go back to
Zinc Binding Sites List in 4ayb
Zinc binding site 4 out
of 10 in the Rnap at 3.2ANG
 Mono view
 Stereo pair view
|
|
A full contact list of Zinc with other atoms in the Zn binding
site number 4 of Rnap at 3.2ANG within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn1883
b:81.4
occ:1.00
|
OD2
|
A:ASP241
|
2.0
|
0.6
|
1.0
|
|
NE2
|
A:HIS237
|
2.0
|
0.9
|
1.0
|
|
CD2
|
A:HIS237
|
2.9
|
0.8
|
1.0
|
|
CE1
|
A:HIS237
|
3.0
|
1.0
|
1.0
|
|
HD2
|
A:HIS237
|
3.1
|
81.4
|
1.0
|
|
CG
|
A:ASP241
|
3.1
|
0.3
|
1.0
|
|
HE1
|
A:HIS237
|
3.3
|
81.4
|
1.0
|
|
OD1
|
A:ASP241
|
3.6
|
0.5
|
1.0
|
|
HG
|
A:SER287
|
3.9
|
81.4
|
1.0
|
|
HZ3
|
A:LYS238
|
3.9
|
81.4
|
1.0
|
|
CG
|
A:HIS237
|
4.1
|
1.0
|
1.0
|
|
ND1
|
A:HIS237
|
4.1
|
0.8
|
1.0
|
|
OG
|
A:SER287
|
4.2
|
84.0
|
1.0
|
|
HD2
|
A:LYS238
|
4.2
|
81.4
|
1.0
|
|
CB
|
A:ASP241
|
4.4
|
0.5
|
1.0
|
|
HD12
|
A:LEU295
|
4.4
|
81.4
|
1.0
|
|
HZ1
|
A:LYS238
|
4.4
|
81.4
|
1.0
|
|
HE1
|
A:HIS272
|
4.5
|
81.4
|
1.0
|
|
HB3
|
A:ASP241
|
4.5
|
81.4
|
1.0
|
|
HB2
|
A:ASP241
|
4.5
|
81.4
|
1.0
|
|
NZ
|
A:LYS238
|
4.6
|
96.7
|
1.0
|
|
HD3
|
A:LYS238
|
4.7
|
81.4
|
1.0
|
|
HA
|
A:LYS238
|
4.7
|
81.4
|
1.0
|
|
HD13
|
A:LEU295
|
4.8
|
81.4
|
1.0
|
|
O
|
A:HIS237
|
4.9
|
0.1
|
1.0
|
|
CD
|
A:LYS238
|
4.9
|
94.0
|
1.0
|
|
HD1
|
A:HIS237
|
4.9
|
81.4
|
1.0
|
|
CE1
|
A:HIS272
|
4.9
|
88.3
|
1.0
|
|
Zinc binding site 5 out
of 10 in 4ayb
Go back to
Zinc Binding Sites List in 4ayb
Zinc binding site 5 out
of 10 in the Rnap at 3.2ANG
 Mono view
 Stereo pair view
|
|
A full contact list of Zinc with other atoms in the Zn binding
site number 5 of Rnap at 3.2ANG within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Zn2126
b:81.4
occ:1.00
|
ND1
|
B:HIS1085
|
2.1
|
74.0
|
1.0
|
|
SG
|
B:CYS1067
|
2.3
|
0.5
|
1.0
|
|
SG
|
B:CYS1064
|
2.3
|
67.0
|
1.0
|
|
SG
|
B:CYS1082
|
2.4
|
73.0
|
1.0
|
|
HB2
|
B:CYS1067
|
2.5
|
81.4
|
1.0
|
|
H
|
B:HIS1085
|
2.9
|
81.4
|
1.0
|
|
CE1
|
B:HIS1085
|
2.9
|
74.8
|
1.0
|
|
CB
|
B:CYS1067
|
2.9
|
99.5
|
1.0
|
|
HB
|
B:ILE1084
|
2.9
|
81.4
|
1.0
|
|
HE1
|
B:HIS1085
|
3.0
|
81.4
|
1.0
|
|
HB2
|
B:CYS1064
|
3.0
|
81.4
|
1.0
|
|
CB
|
B:CYS1064
|
3.1
|
63.7
|
1.0
|
|
CG
|
B:HIS1085
|
3.3
|
76.3
|
1.0
|
|
HB2
|
B:HIS1085
|
3.3
|
81.4
|
1.0
|
|
HB3
|
B:CYS1064
|
3.3
|
81.4
|
1.0
|
|
HG
|
B:SER1089
|
3.4
|
81.4
|
1.0
|
|
HB3
|
B:CYS1067
|
3.4
|
81.4
|
1.0
|
|
N
|
B:HIS1085
|
3.7
|
94.3
|
1.0
|
|
CB
|
B:HIS1085
|
3.7
|
76.3
|
1.0
|
|
HB2
|
B:CYS1082
|
3.8
|
81.4
|
1.0
|
|
CB
|
B:CYS1082
|
3.8
|
70.2
|
1.0
|
|
H
|
B:ILE1084
|
3.8
|
81.4
|
1.0
|
|
CB
|
B:ILE1084
|
3.9
|
72.7
|
1.0
|
|
HG23
|
B:ILE1084
|
4.0
|
81.4
|
1.0
|
|
NE2
|
B:HIS1085
|
4.1
|
77.4
|
1.0
|
|
HB3
|
B:CYS1082
|
4.2
|
81.4
|
1.0
|
|
CA
|
B:CYS1067
|
4.2
|
0.7
|
1.0
|
|
OG
|
B:SER1089
|
4.2
|
0.5
|
1.0
|
|
CD2
|
B:HIS1085
|
4.3
|
78.5
|
1.0
|
|
N
|
B:CYS1067
|
4.3
|
0.5
|
1.0
|
|
H
|
B:CYS1067
|
4.3
|
81.4
|
1.0
|
|
CG2
|
B:ILE1084
|
4.3
|
75.3
|
1.0
|
|
HG22
|
B:ILE1084
|
4.3
|
81.4
|
1.0
|
|
CA
|
B:HIS1085
|
4.3
|
96.0
|
1.0
|
|
N
|
B:ILE1084
|
4.4
|
81.1
|
1.0
|
|
HD11
|
B:ILE1084
|
4.4
|
81.4
|
1.0
|
|
HB2
|
B:TYR1069
|
4.5
|
81.4
|
1.0
|
|
CA
|
B:ILE1084
|
4.5
|
83.7
|
1.0
|
|
HB3
|
B:SER1089
|
4.5
|
81.4
|
1.0
|
|
C
|
B:ILE1084
|
4.5
|
85.5
|
1.0
|
|
CA
|
B:CYS1064
|
4.6
|
50.3
|
1.0
|
|
HG3
|
B:GLN1066
|
4.6
|
81.4
|
1.0
|
|
HB3
|
B:HIS1085
|
4.6
|
81.4
|
1.0
|
|
HA
|
B:CYS1067
|
4.6
|
81.4
|
1.0
|
|
HD2
|
B:PRO1083
|
4.6
|
81.4
|
1.0
|
|
H
|
B:GLN1066
|
4.6
|
81.4
|
1.0
|
|
HG2
|
B:PRO1083
|
4.7
|
81.4
|
1.0
|
|
H
|
B:TYR1069
|
4.7
|
81.4
|
1.0
|
|
HA
|
B:CYS1064
|
4.8
|
81.4
|
1.0
|
|
CB
|
B:SER1089
|
4.8
|
0.9
|
1.0
|
|
HE2
|
B:HIS1085
|
4.8
|
81.4
|
1.0
|
|
CG1
|
B:ILE1084
|
4.9
|
72.0
|
1.0
|
|
HB2
|
B:SER1089
|
4.9
|
81.4
|
1.0
|
|
H
|
B:GLY1068
|
4.9
|
81.4
|
1.0
|
|
C
|
B:GLN1066
|
4.9
|
0.8
|
1.0
|
|
HG12
|
B:ILE1084
|
4.9
|
81.4
|
1.0
|
|
HD2
|
B:TYR1069
|
4.9
|
81.4
|
1.0
|
|
HD22
|
B:LEU1091
|
5.0
|
81.4
|
1.0
|
|
H
|
B:ASP1065
|
5.0
|
81.4
|
1.0
|
|
Zinc binding site 6 out
of 10 in 4ayb
Go back to
Zinc Binding Sites List in 4ayb
Zinc binding site 6 out
of 10 in the Rnap at 3.2ANG
 Mono view
 Stereo pair view
|
|
A full contact list of Zinc with other atoms in the Zn binding
site number 6 of Rnap at 3.2ANG within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Zn2127
b:81.4
occ:1.00
|
ND1
|
B:HIS570
|
2.0
|
80.5
|
1.0
|
|
CE1
|
B:HIS570
|
2.7
|
80.8
|
1.0
|
|
HE1
|
B:HIS570
|
2.8
|
81.4
|
1.0
|
|
CG
|
B:HIS570
|
3.2
|
81.4
|
1.0
|
|
HB3
|
B:HIS570
|
3.2
|
81.4
|
1.0
|
|
HG22
|
B:ILE524
|
3.5
|
81.4
|
1.0
|
|
CB
|
B:HIS570
|
3.7
|
81.5
|
1.0
|
|
OE2
|
B:GLU622
|
3.8
|
65.1
|
1.0
|
|
NE2
|
B:HIS570
|
3.9
|
81.7
|
1.0
|
|
HG23
|
B:ILE524
|
3.9
|
81.4
|
1.0
|
|
HD22
|
B:ASN572
|
4.0
|
81.4
|
1.0
|
|
H
|
B:GLY527
|
4.0
|
81.4
|
1.0
|
|
HA2
|
B:GLY527
|
4.0
|
81.4
|
1.0
|
|
HB
|
B:ILE524
|
4.1
|
81.4
|
1.0
|
|
CG2
|
B:ILE524
|
4.1
|
77.6
|
1.0
|
|
OD1
|
B:ASN572
|
4.1
|
0.2
|
1.0
|
|
CD2
|
B:HIS570
|
4.1
|
82.1
|
1.0
|
|
HH12
|
B:ARG174
|
4.2
|
81.4
|
1.0
|
|
NH1
|
B:ARG174
|
4.3
|
93.9
|
1.0
|
|
HH22
|
B:ARG174
|
4.3
|
81.4
|
1.0
|
|
HB2
|
B:HIS570
|
4.4
|
81.4
|
1.0
|
|
CZ
|
B:ARG174
|
4.5
|
93.8
|
1.0
|
|
NH2
|
B:ARG174
|
4.5
|
93.4
|
1.0
|
|
HA
|
B:HIS570
|
4.5
|
81.4
|
1.0
|
|
N
|
B:GLY527
|
4.5
|
64.8
|
1.0
|
|
HG2
|
B:GLU622
|
4.6
|
81.4
|
1.0
|
|
HE2
|
B:HIS570
|
4.6
|
81.4
|
1.0
|
|
HH11
|
B:ARG174
|
4.7
|
81.4
|
1.0
|
|
ND2
|
B:ASN572
|
4.7
|
99.8
|
1.0
|
|
CB
|
B:ILE524
|
4.7
|
79.3
|
1.0
|
|
CA
|
B:GLY527
|
4.7
|
64.7
|
1.0
|
|
CA
|
B:HIS570
|
4.8
|
86.3
|
1.0
|
|
CG
|
B:ASN572
|
4.8
|
0.2
|
1.0
|
|
HH21
|
B:ARG174
|
4.9
|
81.4
|
1.0
|
|
CD
|
B:GLU622
|
4.9
|
64.6
|
1.0
|
|
HG21
|
B:ILE524
|
5.0
|
81.4
|
1.0
|
|
Zinc binding site 7 out
of 10 in 4ayb
Go back to
Zinc Binding Sites List in 4ayb
Zinc binding site 7 out
of 10 in the Rnap at 3.2ANG
 Mono view
 Stereo pair view
|
|
A full contact list of Zinc with other atoms in the Zn binding
site number 7 of Rnap at 3.2ANG within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Zn2128
b:81.4
occ:1.00
|
HE2
|
B:HIS696
|
2.2
|
81.4
|
1.0
|
|
HD3
|
B:ARG694
|
2.9
|
81.4
|
1.0
|
|
NE2
|
B:HIS696
|
3.0
|
50.5
|
1.0
|
|
HB2
|
B:HIS997
|
3.3
|
81.4
|
1.0
|
|
HD2
|
B:HIS997
|
3.6
|
81.4
|
1.0
|
|
HG3
|
B:ARG694
|
3.6
|
81.4
|
1.0
|
|
CD2
|
B:HIS997
|
3.6
|
48.5
|
1.0
|
|
HE1
|
B:PHE757
|
3.7
|
81.4
|
1.0
|
|
CD
|
B:ARG694
|
3.7
|
89.0
|
1.0
|
|
HD2
|
B:HIS696
|
3.7
|
81.4
|
1.0
|
|
CG
|
B:HIS997
|
3.7
|
48.7
|
1.0
|
|
CD2
|
B:HIS696
|
3.8
|
50.8
|
1.0
|
|
HD2
|
B:ARG694
|
3.8
|
81.4
|
1.0
|
|
CB
|
B:HIS997
|
4.0
|
49.1
|
1.0
|
|
CE1
|
B:HIS696
|
4.0
|
50.6
|
1.0
|
|
CG
|
B:ARG694
|
4.1
|
89.3
|
1.0
|
|
HB2
|
B:ARG694
|
4.2
|
81.4
|
1.0
|
|
HE1
|
B:HIS696
|
4.2
|
81.4
|
1.0
|
|
HB3
|
B:HIS997
|
4.2
|
81.4
|
1.0
|
|
NE2
|
B:HIS997
|
4.3
|
48.3
|
1.0
|
|
ND1
|
B:HIS997
|
4.4
|
48.7
|
1.0
|
|
CE1
|
B:PHE757
|
4.6
|
33.4
|
1.0
|
|
HE2
|
B:HIS997
|
4.7
|
81.4
|
1.0
|
|
CE1
|
B:HIS997
|
4.7
|
48.4
|
1.0
|
|
CB
|
B:ARG694
|
4.7
|
89.6
|
1.0
|
|
O
|
B:ARG694
|
4.8
|
61.9
|
1.0
|
|
HG21
|
B:THR420
|
4.8
|
81.4
|
1.0
|
|
OG1
|
B:THR420
|
4.9
|
62.2
|
1.0
|
|
HD1
|
B:HIS997
|
4.9
|
81.4
|
1.0
|
|
NE
|
B:ARG694
|
4.9
|
89.1
|
1.0
|
|
CG
|
B:HIS696
|
5.0
|
51.2
|
1.0
|
|
HG2
|
B:ARG694
|
5.0
|
81.4
|
1.0
|
|
O
|
B:HIS997
|
5.0
|
32.9
|
1.0
|
|
Zinc binding site 8 out
of 10 in 4ayb
Go back to
Zinc Binding Sites List in 4ayb
Zinc binding site 8 out
of 10 in the Rnap at 3.2ANG
 Mono view
 Stereo pair view
|
|
A full contact list of Zinc with other atoms in the Zn binding
site number 8 of Rnap at 3.2ANG within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Zn1395
b:81.4
occ:1.00
|
HE1
|
C:HIS353
|
1.2
|
81.4
|
1.0
|
|
CE1
|
C:HIS353
|
1.7
|
95.7
|
1.0
|
|
HE2
|
C:HIS353
|
1.9
|
81.4
|
1.0
|
|
NE2
|
C:HIS353
|
2.0
|
97.7
|
1.0
|
|
ND1
|
C:HIS353
|
3.0
|
95.6
|
1.0
|
|
HG22
|
C:VAL349
|
3.3
|
81.4
|
1.0
|
|
CD2
|
C:HIS353
|
3.4
|
98.8
|
1.0
|
|
HD1
|
C:HIS353
|
3.5
|
81.4
|
1.0
|
|
HA
|
C:ARG331
|
3.6
|
81.4
|
1.0
|
|
CG
|
C:HIS353
|
3.8
|
97.5
|
1.0
|
|
HB3
|
C:ARG344
|
3.8
|
81.4
|
1.0
|
|
HB
|
C:VAL349
|
3.9
|
81.4
|
1.0
|
|
HG2
|
C:ARG331
|
3.9
|
81.4
|
1.0
|
|
HG2
|
C:ARG344
|
4.0
|
81.4
|
1.0
|
|
HA2
|
C:GLY336
|
4.0
|
81.4
|
1.0
|
|
CG2
|
C:VAL349
|
4.0
|
0.5
|
1.0
|
|
HD2
|
C:HIS353
|
4.1
|
81.4
|
1.0
|
|
HG21
|
C:VAL349
|
4.1
|
81.4
|
1.0
|
|
HE
|
C:ARG344
|
4.1
|
81.4
|
1.0
|
|
HG12
|
C:VAL349
|
4.2
|
81.4
|
1.0
|
|
O
|
C:ARG331
|
4.3
|
0.7
|
1.0
|
|
O
|
C:GLU348
|
4.4
|
57.2
|
1.0
|
|
CB
|
C:VAL349
|
4.4
|
0.0
|
1.0
|
|
CA
|
C:ARG331
|
4.4
|
0.4
|
1.0
|
|
HD2
|
C:ARG331
|
4.5
|
81.4
|
1.0
|
|
HB3
|
C:ARG331
|
4.5
|
81.4
|
1.0
|
|
CG
|
C:ARG331
|
4.7
|
0.1
|
1.0
|
|
CB
|
C:ARG344
|
4.7
|
86.6
|
1.0
|
|
CG
|
C:ARG344
|
4.7
|
86.3
|
1.0
|
|
C
|
C:ARG331
|
4.8
|
0.1
|
1.0
|
|
CB
|
C:ARG331
|
4.8
|
0.0
|
1.0
|
|
HA3
|
C:GLY336
|
4.8
|
81.4
|
1.0
|
|
CG1
|
C:VAL349
|
4.8
|
0.4
|
1.0
|
|
HG23
|
C:VAL349
|
4.8
|
81.4
|
1.0
|
|
NE
|
C:ARG344
|
4.9
|
89.7
|
1.0
|
|
CA
|
C:GLY336
|
4.9
|
85.0
|
1.0
|
|
CD
|
C:ARG331
|
5.0
|
0.7
|
1.0
|
|
Zinc binding site 9 out
of 10 in 4ayb
Go back to
Zinc Binding Sites List in 4ayb
Zinc binding site 9 out
of 10 in the Rnap at 3.2ANG
 Mono view
 Stereo pair view
|
|
A full contact list of Zinc with other atoms in the Zn binding
site number 9 of Rnap at 3.2ANG within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
N:Zn1066
b:88.7
occ:1.00
|
HG
|
N:CYS10
|
2.0
|
81.4
|
1.0
|
|
SG
|
N:CYS45
|
2.1
|
1.0
|
1.0
|
|
SG
|
N:CYS44
|
2.1
|
74.5
|
1.0
|
|
SG
|
N:CYS10
|
2.2
|
0.3
|
1.0
|
|
SG
|
N:CYS7
|
2.3
|
85.8
|
1.0
|
|
HB2
|
N:CYS10
|
2.4
|
81.4
|
1.0
|
|
N
|
N:CYS45
|
2.5
|
0.5
|
1.0
|
|
HB2
|
N:CYS45
|
2.6
|
81.4
|
1.0
|
|
CB
|
N:CYS45
|
2.7
|
0.5
|
1.0
|
|
CB
|
N:CYS10
|
2.8
|
0.2
|
1.0
|
|
CA
|
N:CYS45
|
3.0
|
0.0
|
1.0
|
|
H
|
N:CYS10
|
3.3
|
81.4
|
1.0
|
|
HA
|
N:CYS45
|
3.3
|
81.4
|
1.0
|
|
CB
|
N:CYS44
|
3.3
|
72.7
|
1.0
|
|
HB2
|
N:CYS44
|
3.3
|
81.4
|
1.0
|
|
HB3
|
N:CYS10
|
3.4
|
81.4
|
1.0
|
|
HE
|
N:ARG42
|
3.5
|
81.4
|
1.0
|
|
C
|
N:CYS44
|
3.5
|
63.0
|
1.0
|
|
HB3
|
N:CYS45
|
3.6
|
81.4
|
1.0
|
|
CB
|
N:CYS7
|
3.6
|
87.6
|
1.0
|
|
HB3
|
N:CYS7
|
3.7
|
81.4
|
1.0
|
|
HB2
|
N:ARG42
|
3.7
|
81.4
|
1.0
|
|
HB2
|
N:CYS7
|
3.8
|
81.4
|
1.0
|
|
HB
|
N:THR9
|
3.9
|
81.4
|
1.0
|
|
CA
|
N:CYS44
|
3.9
|
61.7
|
1.0
|
|
N
|
N:CYS10
|
3.9
|
59.4
|
1.0
|
|
CA
|
N:CYS10
|
4.0
|
61.4
|
1.0
|
|
H
|
N:GLY11
|
4.0
|
81.4
|
1.0
|
|
H
|
N:CYS44
|
4.1
|
81.4
|
1.0
|
|
HB3
|
N:CYS44
|
4.1
|
81.4
|
1.0
|
|
HB3
|
N:ARG42
|
4.2
|
81.4
|
1.0
|
|
NE
|
N:ARG42
|
4.3
|
98.2
|
1.0
|
|
N
|
N:CYS44
|
4.4
|
63.5
|
1.0
|
|
HG
|
N:SER12
|
4.4
|
81.4
|
1.0
|
|
CB
|
N:ARG42
|
4.4
|
98.3
|
1.0
|
|
C
|
N:CYS45
|
4.4
|
0.6
|
1.0
|
|
O
|
N:PHE8
|
4.5
|
97.9
|
1.0
|
|
O
|
N:CYS44
|
4.5
|
62.7
|
1.0
|
|
OG
|
N:SER12
|
4.5
|
0.1
|
1.0
|
|
HH21
|
N:ARG42
|
4.5
|
81.4
|
1.0
|
|
HD2
|
N:ARG42
|
4.5
|
81.4
|
1.0
|
|
H
|
N:SER12
|
4.5
|
81.4
|
1.0
|
|
HA
|
N:CYS10
|
4.6
|
81.4
|
1.0
|
|
H
|
N:ARG46
|
4.6
|
81.4
|
1.0
|
|
N
|
N:GLY11
|
4.7
|
51.2
|
1.0
|
|
CB
|
N:THR9
|
4.8
|
41.4
|
1.0
|
|
HA
|
N:CYS44
|
4.8
|
81.4
|
1.0
|
|
HH21
|
N:ARG47
|
4.8
|
81.4
|
1.0
|
|
C
|
N:CYS10
|
4.8
|
62.6
|
1.0
|
|
HG23
|
N:THR9
|
4.8
|
81.4
|
1.0
|
|
CD
|
N:ARG42
|
4.9
|
97.4
|
1.0
|
|
N
|
N:ARG46
|
4.9
|
59.2
|
1.0
|
|
HG22
|
N:THR9
|
5.0
|
81.4
|
1.0
|
|
O
|
N:ARG42
|
5.0
|
76.4
|
1.0
|
|
HD12
|
N:ILE14
|
5.0
|
81.4
|
1.0
|
|
Zinc binding site 10 out
of 10 in 4ayb
Go back to
Zinc Binding Sites List in 4ayb
Zinc binding site 10 out
of 10 in the Rnap at 3.2ANG
 Mono view
 Stereo pair view
|
|
A full contact list of Zinc with other atoms in the Zn binding
site number 10 of Rnap at 3.2ANG within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
P:Zn1049
b:0.3
occ:1.00
|
HG22
|
P:THR12
|
1.5
|
81.4
|
1.0
|
|
OG1
|
P:THR12
|
2.0
|
1.0
|
1.0
|
|
CG2
|
P:THR12
|
2.2
|
0.3
|
1.0
|
|
SG
|
P:CYS26
|
2.2
|
55.4
|
1.0
|
|
CB
|
P:THR12
|
2.3
|
0.9
|
1.0
|
|
SG
|
P:CYS29
|
2.3
|
0.1
|
1.0
|
|
HB
|
P:THR12
|
2.4
|
81.4
|
1.0
|
|
SG
|
P:CYS9
|
2.4
|
0.4
|
1.0
|
|
HB2
|
P:TYR28
|
2.5
|
81.4
|
1.0
|
|
HB2
|
P:CYS29
|
2.7
|
81.4
|
1.0
|
|
HG21
|
P:THR12
|
2.7
|
81.4
|
1.0
|
|
HG23
|
P:THR12
|
2.9
|
81.4
|
1.0
|
|
CB
|
P:CYS29
|
3.0
|
0.9
|
1.0
|
|
H
|
P:CYS29
|
3.0
|
81.4
|
1.0
|
|
N
|
P:CYS29
|
3.3
|
0.3
|
1.0
|
|
CB
|
P:TYR28
|
3.5
|
0.8
|
1.0
|
|
HD1
|
P:TYR28
|
3.6
|
81.4
|
1.0
|
|
CA
|
P:CYS29
|
3.7
|
0.1
|
1.0
|
|
CA
|
P:THR12
|
3.8
|
0.4
|
1.0
|
|
HB3
|
P:CYS29
|
3.8
|
81.4
|
1.0
|
|
C
|
P:TYR28
|
3.9
|
96.1
|
1.0
|
|
CB
|
P:CYS26
|
3.9
|
53.6
|
1.0
|
|
O
|
P:TRP10
|
3.9
|
0.9
|
1.0
|
|
HB3
|
P:TYR28
|
3.9
|
81.4
|
1.0
|
|
H
|
P:TYR28
|
4.0
|
81.4
|
1.0
|
|
HB3
|
P:CYS26
|
4.1
|
81.4
|
1.0
|
|
HA
|
P:CYS29
|
4.1
|
81.4
|
1.0
|
|
CA
|
P:TYR28
|
4.1
|
96.1
|
1.0
|
|
O
|
P:LYS8
|
4.2
|
93.4
|
1.0
|
|
HB
|
P:THR14
|
4.2
|
81.4
|
1.0
|
|
HB2
|
P:CYS26
|
4.2
|
81.4
|
1.0
|
|
HG1
|
P:THR14
|
4.2
|
81.4
|
1.0
|
|
CB
|
P:CYS9
|
4.2
|
0.8
|
1.0
|
|
HA
|
P:THR12
|
4.2
|
81.4
|
1.0
|
|
CD1
|
P:TYR28
|
4.3
|
0.6
|
1.0
|
|
CG
|
P:TYR28
|
4.3
|
0.5
|
1.0
|
|
H
|
P:THR14
|
4.3
|
81.4
|
1.0
|
|
N
|
P:THR12
|
4.4
|
0.5
|
1.0
|
|
OG1
|
P:THR14
|
4.4
|
0.2
|
1.0
|
|
H
|
P:PHE13
|
4.4
|
81.4
|
1.0
|
|
N
|
P:TYR28
|
4.4
|
94.5
|
1.0
|
|
HB3
|
P:CYS9
|
4.5
|
81.4
|
1.0
|
|
C
|
P:THR12
|
4.6
|
0.6
|
1.0
|
|
HB2
|
P:CYS9
|
4.6
|
81.4
|
1.0
|
|
H
|
P:THR12
|
4.7
|
81.4
|
1.0
|
|
O
|
P:TYR28
|
4.7
|
97.7
|
1.0
|
|
N
|
P:PHE13
|
4.7
|
87.4
|
1.0
|
|
CB
|
P:THR14
|
4.8
|
0.1
|
1.0
|
|
HB2
|
P:TYR31
|
4.8
|
81.4
|
1.0
|
|
H
|
P:TRP10
|
4.8
|
81.4
|
1.0
|
|
O
|
P:LYS11
|
4.8
|
0.8
|
1.0
|
|
C
|
P:LYS11
|
4.9
|
0.1
|
1.0
|
|
HG3
|
P:LYS11
|
4.9
|
81.4
|
1.0
|
|
C
|
P:CYS29
|
5.0
|
0.3
|
1.0
|
|
Reference:
M.N.Wojtas,
M.Mogni,
O.Millet,
S.D.Bell,
N.G.A.Abrescia.
Structural and Functional Analyses of the Interaction of Archaeal Rna Polymerase with Dna. Nucleic Acids Res. V. 40 9941 2012.
ISSN: ISSN 0305-1048
PubMed: 22848102
DOI: 10.1093/NAR/GKS692
Page generated: Sat Oct 26 19:29:48 2024
|
