Zinc in PDB 6tmf: Structure of An Archaeal ABCE1-Bound Ribosomal Post-Splitting Complex
Other elements in 6tmf:
The structure of Structure of An Archaeal ABCE1-Bound Ribosomal Post-Splitting Complex also contains other interesting chemical elements:
Zinc Binding Sites:
The binding sites of Zinc atom in the Structure of An Archaeal ABCE1-Bound Ribosomal Post-Splitting Complex
(pdb code 6tmf). This binding sites where shown within
5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the
Structure of An Archaeal ABCE1-Bound Ribosomal Post-Splitting Complex, PDB code: 6tmf:
Jump to Zinc binding site number:
1;
2;
3;
4;
Zinc binding site 1 out
of 4 in 6tmf
Go back to
Zinc Binding Sites List in 6tmf
Zinc binding site 1 out
of 4 in the Structure of An Archaeal ABCE1-Bound Ribosomal Post-Splitting Complex
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 1 of Structure of An Archaeal ABCE1-Bound Ribosomal Post-Splitting Complex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
Q:Zn101
b:36.6
occ:1.00
|
SG
|
Q:CYS39
|
2.5
|
14.6
|
1.0
|
SG
|
Q:CYS24
|
2.5
|
16.7
|
1.0
|
SG
|
Q:CYS21
|
2.5
|
15.6
|
1.0
|
SG
|
Q:CYS42
|
2.5
|
14.6
|
1.0
|
CB
|
Q:CYS42
|
3.0
|
14.6
|
1.0
|
CB
|
Q:CYS39
|
3.3
|
14.6
|
1.0
|
N
|
Q:CYS24
|
3.5
|
16.7
|
1.0
|
CB
|
Q:CYS24
|
3.5
|
16.7
|
1.0
|
CB
|
Q:CYS21
|
3.6
|
15.6
|
1.0
|
N
|
Q:CYS39
|
3.8
|
14.6
|
1.0
|
CB
|
Q:ARG23
|
3.8
|
16.0
|
1.0
|
CA
|
Q:CYS24
|
4.1
|
16.7
|
1.0
|
CA
|
Q:CYS39
|
4.1
|
14.6
|
1.0
|
CA
|
Q:CYS42
|
4.2
|
14.6
|
1.0
|
N
|
Q:CYS42
|
4.3
|
14.6
|
1.0
|
O
|
Q:CYS39
|
4.5
|
14.6
|
1.0
|
C
|
Q:ARG23
|
4.5
|
16.0
|
1.0
|
CA
|
Q:ARG23
|
4.6
|
16.0
|
1.0
|
C
|
Q:CYS39
|
4.7
|
14.6
|
1.0
|
N
|
Q:GLY25
|
4.8
|
16.1
|
1.0
|
N
|
Q:ARG23
|
4.8
|
16.0
|
1.0
|
CG
|
Q:ARG23
|
4.9
|
16.0
|
1.0
|
C
|
Q:CYS24
|
5.0
|
16.7
|
1.0
|
C
|
Q:LEU38
|
5.0
|
15.2
|
1.0
|
CD2
|
Q:LEU38
|
5.0
|
15.2
|
1.0
|
|
Zinc binding site 2 out
of 4 in 6tmf
Go back to
Zinc Binding Sites List in 6tmf
Zinc binding site 2 out
of 4 in the Structure of An Archaeal ABCE1-Bound Ribosomal Post-Splitting Complex
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 2 of Structure of An Archaeal ABCE1-Bound Ribosomal Post-Splitting Complex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
W:Zn101
b:40.9
occ:1.00
|
CB
|
W:CYS31
|
2.0
|
26.3
|
1.0
|
SG
|
W:CYS54
|
2.2
|
24.4
|
1.0
|
SG
|
W:CYS51
|
2.3
|
20.6
|
1.0
|
SG
|
W:CYS28
|
2.3
|
21.1
|
1.0
|
SG
|
W:CYS31
|
2.4
|
26.3
|
1.0
|
CB
|
W:CYS28
|
2.8
|
21.1
|
1.0
|
CB
|
W:CYS51
|
3.4
|
20.6
|
1.0
|
CA
|
W:CYS31
|
3.5
|
26.3
|
1.0
|
O
|
W:GLY32
|
3.6
|
24.1
|
1.0
|
CB
|
W:CYS54
|
3.7
|
24.4
|
1.0
|
N
|
W:CYS54
|
3.9
|
24.4
|
1.0
|
CB
|
W:ALA34
|
4.1
|
20.7
|
1.0
|
N
|
W:CYS31
|
4.1
|
26.3
|
1.0
|
C
|
W:CYS31
|
4.1
|
26.3
|
1.0
|
CA
|
W:CYS28
|
4.3
|
21.1
|
1.0
|
CA
|
W:CYS54
|
4.4
|
24.4
|
1.0
|
N
|
W:GLY32
|
4.4
|
24.1
|
1.0
|
CB
|
W:LYS53
|
4.4
|
25.0
|
1.0
|
C
|
W:GLY32
|
4.7
|
24.1
|
1.0
|
CA
|
W:CYS51
|
4.8
|
20.6
|
1.0
|
C
|
W:CYS28
|
4.9
|
21.1
|
1.0
|
O
|
W:CYS31
|
4.9
|
26.3
|
1.0
|
O
|
W:PRO29
|
4.9
|
20.6
|
1.0
|
C
|
W:LYS53
|
5.0
|
25.0
|
1.0
|
|
Zinc binding site 3 out
of 4 in 6tmf
Go back to
Zinc Binding Sites List in 6tmf
Zinc binding site 3 out
of 4 in the Structure of An Archaeal ABCE1-Bound Ribosomal Post-Splitting Complex
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 3 of Structure of An Archaeal ABCE1-Bound Ribosomal Post-Splitting Complex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
W:Zn102
b:41.8
occ:1.00
|
SG
|
W:CYS13
|
2.2
|
18.8
|
1.0
|
SG
|
W:CYS10
|
2.2
|
15.9
|
1.0
|
SG
|
W:CYS42
|
2.3
|
13.6
|
1.0
|
SG
|
W:CYS39
|
2.6
|
14.2
|
1.0
|
CB
|
W:CYS13
|
2.8
|
18.8
|
1.0
|
CB
|
W:CYS10
|
3.0
|
15.9
|
1.0
|
N
|
W:CYS13
|
3.1
|
18.8
|
1.0
|
CB
|
W:CYS42
|
3.4
|
13.6
|
1.0
|
CA
|
W:CYS13
|
3.5
|
18.8
|
1.0
|
CB
|
W:CYS39
|
3.8
|
14.2
|
1.0
|
CB
|
W:SER12
|
3.8
|
16.4
|
1.0
|
C
|
W:SER12
|
4.1
|
16.4
|
1.0
|
N
|
W:CYS39
|
4.1
|
14.2
|
1.0
|
CA
|
W:SER12
|
4.4
|
16.4
|
1.0
|
N
|
W:SER12
|
4.4
|
16.4
|
1.0
|
CA
|
W:CYS10
|
4.5
|
15.9
|
1.0
|
C
|
W:CYS13
|
4.5
|
18.8
|
1.0
|
CA
|
W:CYS39
|
4.5
|
14.2
|
1.0
|
N
|
W:GLY14
|
4.6
|
17.4
|
1.0
|
CA
|
W:CYS42
|
4.7
|
13.6
|
1.0
|
OG
|
W:SER12
|
4.7
|
16.4
|
1.0
|
N
|
W:CYS42
|
4.8
|
13.6
|
1.0
|
C
|
W:CYS10
|
5.0
|
15.9
|
1.0
|
|
Zinc binding site 4 out
of 4 in 6tmf
Go back to
Zinc Binding Sites List in 6tmf
Zinc binding site 4 out
of 4 in the Structure of An Archaeal ABCE1-Bound Ribosomal Post-Splitting Complex
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 4 of Structure of An Archaeal ABCE1-Bound Ribosomal Post-Splitting Complex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
Y:Zn101
b:40.9
occ:1.00
|
SG
|
Y:CYS42
|
2.2
|
26.4
|
1.0
|
CB
|
Y:CYS20
|
2.2
|
28.5
|
1.0
|
SG
|
Y:CYS20
|
2.2
|
28.5
|
1.0
|
SG
|
Y:CYS39
|
2.3
|
25.4
|
1.0
|
CB
|
Y:CYS39
|
3.1
|
25.4
|
1.0
|
OD1
|
Y:ASN25
|
3.2
|
27.2
|
1.0
|
CA
|
Y:CYS20
|
3.7
|
28.5
|
1.0
|
CB
|
Y:CYS42
|
3.9
|
26.4
|
1.0
|
CB
|
Y:CYS23
|
3.9
|
30.7
|
1.0
|
N
|
Y:CYS23
|
4.1
|
30.7
|
1.0
|
CG2
|
Y:VAL41
|
4.1
|
26.4
|
1.0
|
CG
|
Y:ASN25
|
4.3
|
27.2
|
1.0
|
N
|
Y:CYS20
|
4.3
|
28.5
|
1.0
|
CB
|
Y:ALA44
|
4.4
|
24.5
|
1.0
|
CA
|
Y:CYS39
|
4.5
|
25.4
|
1.0
|
CA
|
Y:CYS23
|
4.5
|
30.7
|
1.0
|
C
|
Y:CYS20
|
4.6
|
28.5
|
1.0
|
N
|
Y:CYS42
|
4.6
|
26.4
|
1.0
|
SG
|
Y:CYS23
|
4.6
|
30.7
|
1.0
|
CD2
|
Y:LEU46
|
4.6
|
22.9
|
1.0
|
ND2
|
Y:ASN25
|
4.6
|
27.2
|
1.0
|
N
|
Y:GLY24
|
4.7
|
27.9
|
1.0
|
CA
|
Y:CYS42
|
4.8
|
26.4
|
1.0
|
CB
|
Y:ASP22
|
4.8
|
30.4
|
1.0
|
N
|
Y:ASP22
|
4.9
|
30.4
|
1.0
|
|
Reference:
E.Nuerenberg Goloub,
H.Kratzat,
H.Heinemann,
A.Heuer,
P.Koetter,
O.Berninghausen,
T.Becker,
R.Tampe,
R.Beckmann.
Molecular Analysis of the Ribosome Recycling Factor ABCE1 Bound to the 30S Post-Splitting Complex Embo J. 2020.
ISSN: ESSN 1460-2075
DOI: 10.15252/EMBJ.2019103788
Page generated: Tue Oct 29 08:05:08 2024
|