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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:

Magnesium (Mg) 29 atoms
Iron (Fe) 8 atoms

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

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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

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