Zinc in PDB 7of0: Structure of A Human Mitochondrial Ribosome Large Subunit Assembly Intermediate in Complex with MTERF4-NSUN4 (DATASET1).

Enzymatic activity of Structure of A Human Mitochondrial Ribosome Large Subunit Assembly Intermediate in Complex with MTERF4-NSUN4 (DATASET1).

All present enzymatic activity of Structure of A Human Mitochondrial Ribosome Large Subunit Assembly Intermediate in Complex with MTERF4-NSUN4 (DATASET1).:
3.1.1.29;

Other elements in 7of0:

The structure of Structure of A Human Mitochondrial Ribosome Large Subunit Assembly Intermediate in Complex with MTERF4-NSUN4 (DATASET1). also contains other interesting chemical elements:

Magnesium (Mg) 61 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Structure of A Human Mitochondrial Ribosome Large Subunit Assembly Intermediate in Complex with MTERF4-NSUN4 (DATASET1). (pdb code 7of0). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the Structure of A Human Mitochondrial Ribosome Large Subunit Assembly Intermediate in Complex with MTERF4-NSUN4 (DATASET1)., PDB code: 7of0:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in 7of0

Go back to Zinc Binding Sites List in 7of0
Zinc binding site 1 out of 3 in the Structure of A Human Mitochondrial Ribosome Large Subunit Assembly Intermediate in Complex with MTERF4-NSUN4 (DATASET1).


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of A Human Mitochondrial Ribosome Large Subunit Assembly Intermediate in Complex with MTERF4-NSUN4 (DATASET1). within 5.0Å range:
probe atom residue distance (Å) B Occ
0:Zn200

b:111.5
occ:1.00
 SG 0:CYS113 2.3 97.5 1.0
SG 0:CYS126 2.3 84.9 1.0
SG 0:CYS123 2.3 78.9 1.0
SG 0:CYS110 2.3 91.3 1.0
CB 0:CYS123 3.1 78.9 1.0
CB 0:CYS110 3.2 91.3 1.0
CB 0:CYS126 3.7 84.9 1.0
CB 0:CYS113 3.8 97.5 1.0
CB 0:HIS115 4.2 89.0 1.0
N 0:CYS113 4.3 97.5 1.0
ND1 0:HIS115 4.3 89.0 1.0
N 0:CYS126 4.3 84.9 1.0
CA 0:CYS123 4.6 78.9 1.0
CG 0:HIS115 4.6 89.0 1.0
CA 0:CYS113 4.6 97.5 1.0
CA 0:CYS126 4.6 84.9 1.0
CA 0:CYS110 4.7 91.3 1.0
N 0:HIS115 4.7 89.0 1.0
CB 0:GLU112 4.8 99.0 1.0

Zinc binding site 2 out of 3 in 7of0

Go back to Zinc Binding Sites List in 7of0
Zinc binding site 2 out of 3 in the Structure of A Human Mitochondrial Ribosome Large Subunit Assembly Intermediate in Complex with MTERF4-NSUN4 (DATASET1).


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of A Human Mitochondrial Ribosome Large Subunit Assembly Intermediate in Complex with MTERF4-NSUN4 (DATASET1). within 5.0Å range:
probe atom residue distance (Å) B Occ
4:Zn200

b:131.5
occ:1.00
 ND1 4:HIS98 2.1 125.9 1.0
SG 4:CYS76 2.3 134.8 1.0
SG 4:CYS92 2.3 116.1 1.0
SG 4:CYS79 2.3 121.8 1.0
CE1 4:HIS98 2.9 125.9 1.0
CG 4:HIS98 3.1 125.9 1.0
CB 4:CYS92 3.2 116.1 1.0
ND1 4:HIS95 3.3 122.9 1.0
CB 4:CYS76 3.5 134.8 1.0
CB 4:HIS98 3.6 125.9 1.0
CB 4:HIS95 3.8 122.9 1.0
N 4:CYS76 3.8 134.8 1.0
CB 4:CYS79 3.8 121.8 1.0
N 4:CYS79 3.8 121.8 1.0
CG 4:HIS95 4.0 122.9 1.0
NE2 4:HIS98 4.0 125.9 1.0
OG1 4:THR94 4.1 119.1 1.0
CA 4:CYS79 4.1 121.8 1.0
CA 4:CYS76 4.1 134.8 1.0
CD2 4:HIS98 4.1 125.9 1.0
O 4:HIS95 4.2 122.9 1.0
C 4:ASP78 4.4 128.2 1.0
N 4:HIS95 4.4 122.9 1.0
CE1 4:HIS95 4.4 122.9 1.0
C 4:CYS76 4.5 134.8 1.0
CA 4:HIS95 4.5 122.9 1.0
CA 4:CYS92 4.5 116.1 1.0
O 4:CYS76 4.7 134.8 1.0
C 4:HIS95 4.8 122.9 1.0
N 4:ASP78 4.8 128.2 1.0
CB 4:ARG75 4.8 141.4 1.0
C 4:ARG75 4.9 141.4 1.0
O 4:ASP78 4.9 128.2 1.0
CB 4:ASP78 4.9 128.2 1.0
CA 4:ASP78 4.9 128.2 1.0

Zinc binding site 3 out of 3 in 7of0

Go back to Zinc Binding Sites List in 7of0
Zinc binding site 3 out of 3 in the Structure of A Human Mitochondrial Ribosome Large Subunit Assembly Intermediate in Complex with MTERF4-NSUN4 (DATASET1).


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structure of A Human Mitochondrial Ribosome Large Subunit Assembly Intermediate in Complex with MTERF4-NSUN4 (DATASET1). within 5.0Å range:
probe atom residue distance (Å) B Occ
r:Zn301

b:132.0
occ:1.00
 SG r:CYS73 2.3 117.4 1.0
SG r:CYS108 2.3 105.2 1.0
SG I:CYS64 2.3 136.4 1.0
SG r:CYS70 2.3 118.0 1.0
OE1 r:GLN69 2.8 125.8 1.0
CB I:CYS64 3.0 136.4 1.0
N r:CYS70 3.2 118.0 1.0
CB r:GLN69 3.2 125.8 1.0
CB r:CYS70 3.3 118.0 1.0
CA I:CYS64 3.3 136.4 1.0
CB r:CYS73 3.5 117.4 1.0
CD r:GLN69 3.7 125.8 1.0
CA r:CYS70 3.9 118.0 1.0
CG r:GLN69 3.9 125.8 1.0
C r:GLN69 4.1 125.8 1.0
CB r:CYS108 4.1 105.2 1.0
CA r:GLN69 4.1 125.8 1.0
O I:CYS64 4.2 136.4 1.0
C I:CYS64 4.3 136.4 1.0
N I:CYS64 4.3 136.4 1.0
N r:GLN69 4.5 125.8 1.0
N r:CYS73 4.5 117.4 1.0
CA r:CYS73 4.6 117.4 1.0
C r:CYS70 4.8 118.0 1.0
NE2 r:GLN69 4.8 125.8 1.0
O r:CYS70 4.8 118.0 1.0
O I:SER63 4.9 141.7 1.0
C I:SER63 5.0 141.7 1.0
OE2 r:GLU110 5.0 104.9 1.0

Reference:

H.S.Hillen, E.Lavdovskaia, F.Nadler, E.Hanitsch, A.Linden, K.E.Bohnsack, H.Urlaub, R.Richter-Dennerlein. Structural Basis of Gtpase-Mediated Mitochondrial Ribosome Biogenesis and Recycling Nat Commun 2021.
ISSN: ESSN 2041-1723
Page generated: Wed Oct 30 08:29:33 2024

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