Zinc in PDB 8cvm: Cutibacterium Acnes 50S Ribosomal Subunit with P-Site Trna and Sarecycline Bound in the Local Refined Map

Other elements in 8cvm:

The structure of Cutibacterium Acnes 50S Ribosomal Subunit with P-Site Trna and Sarecycline Bound in the Local Refined Map also contains other interesting chemical elements:

Magnesium (Mg) 305 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Cutibacterium Acnes 50S Ribosomal Subunit with P-Site Trna and Sarecycline Bound in the Local Refined Map (pdb code 8cvm). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Cutibacterium Acnes 50S Ribosomal Subunit with P-Site Trna and Sarecycline Bound in the Local Refined Map, PDB code: 8cvm:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 8cvm

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Zinc binding site 1 out of 4 in the Cutibacterium Acnes 50S Ribosomal Subunit with P-Site Trna and Sarecycline Bound in the Local Refined Map


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Cutibacterium Acnes 50S Ribosomal Subunit with P-Site Trna and Sarecycline Bound in the Local Refined Map within 5.0Å range:
probe atom residue distance (Å) B Occ
w:Zn101

b:73.2
occ:1.00
 O w:ILE7 2.2 56.5 1.0
SG w:CYS5 2.2 53.0 1.0
SG w:CYS53 2.3 54.7 1.0
SG w:CYS50 2.3 52.4 1.0
SG w:CYS8 2.3 55.2 1.0
CB w:CYS5 3.1 53.0 1.0
C w:ILE7 3.4 56.5 1.0
CB w:CYS53 3.5 54.7 1.0
CB w:CYS8 3.5 55.2 1.0
CB w:CYS50 3.5 52.4 1.0
N w:CYS50 4.2 52.4 1.0
N w:CYS8 4.2 55.2 1.0
CA w:CYS8 4.3 55.2 1.0
CA w:ILE7 4.4 56.5 1.0
N w:CYS53 4.4 54.7 1.0
CA w:CYS50 4.4 52.4 1.0
CB w:ILE7 4.4 56.5 1.0
CB w:LYS10 4.4 48.6 1.0
CA w:CYS53 4.5 54.7 1.0
CA w:CYS5 4.5 53.0 1.0
N w:ILE7 4.6 56.5 1.0
CE w:LYS10 4.6 48.6 1.0
C w:CYS8 4.7 55.2 1.0
N w:LYS10 4.8 48.6 1.0
N w:ALA9 4.8 51.2 1.0
O w:CYS50 4.9 52.4 1.0
CG2 w:ILE7 4.9 56.5 1.0
C w:CYS5 5.0 53.0 1.0

Zinc binding site 2 out of 4 in 8cvm

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Zinc binding site 2 out of 4 in the Cutibacterium Acnes 50S Ribosomal Subunit with P-Site Trna and Sarecycline Bound in the Local Refined Map


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Cutibacterium Acnes 50S Ribosomal Subunit with P-Site Trna and Sarecycline Bound in the Local Refined Map within 5.0Å range:
probe atom residue distance (Å) B Occ
z:Zn101

b:82.0
occ:1.00
 SG z:CYS30 2.3 63.7 1.0
SG z:CYS48 2.3 64.4 1.0
SG z:CYS35 2.3 67.0 1.0
SG z:CYS45 2.3 60.7 1.0
CB z:CYS35 2.9 67.0 1.0
CB z:CYS45 3.0 60.7 1.0
CB z:CYS30 3.0 63.7 1.0
CB z:CYS48 3.1 64.4 1.0
N z:CYS48 3.7 64.4 1.0
CA z:CYS48 4.0 64.4 1.0
NH2 z:ARG57 4.2 64.0 1.0
CA z:CYS35 4.4 67.0 1.0
CA z:CYS30 4.5 63.7 1.0
CA z:CYS45 4.5 60.7 1.0
CB z:ASN32 4.5 67.0 1.0
CB z:GLU37 4.7 65.3 1.0
N z:GLU37 4.7 65.3 1.0
CB z:SER47 4.7 62.7 1.0
C z:CYS35 4.7 67.0 1.0
N z:GLY36 4.8 64.9 1.0
C z:SER47 4.9 62.7 1.0
C z:CYS48 4.9 64.4 1.0

Zinc binding site 3 out of 4 in 8cvm

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Zinc binding site 3 out of 4 in the Cutibacterium Acnes 50S Ribosomal Subunit with P-Site Trna and Sarecycline Bound in the Local Refined Map


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Cutibacterium Acnes 50S Ribosomal Subunit with P-Site Trna and Sarecycline Bound in the Local Refined Map within 5.0Å range:
probe atom residue distance (Å) B Occ
0:Zn101

b:101.9
occ:1.00
 SG 0:CYS46 2.2 75.7 1.0
SG 0:CYS16 2.3 82.2 1.0
SG 0:CYS43 2.3 72.1 1.0
SG 0:CYS19 2.5 81.4 1.0
CB 0:CYS16 2.5 82.2 1.0
CB 0:CYS43 3.1 72.1 1.0
N 0:CYS19 3.4 81.4 1.0
OG1 0:THR50 3.5 72.7 1.0
CB 0:CYS46 3.7 75.7 1.0
CB 0:CYS19 3.8 81.4 1.0
CA 0:CYS16 4.0 82.2 1.0
CA 0:CYS19 4.1 81.4 1.0
CB 0:GLU18 4.1 83.8 1.0
CB 0:THR50 4.4 72.7 1.0
ND2 0:ASN23 4.4 70.9 1.0
CG2 0:THR50 4.5 72.7 1.0
C 0:GLU18 4.5 83.8 1.0
N 0:GLU18 4.5 83.8 1.0
N 0:CYS46 4.5 75.7 1.0
C 0:CYS16 4.5 82.2 1.0
CA 0:CYS43 4.6 72.1 1.0
CA 0:GLU18 4.6 83.8 1.0
C 0:CYS19 4.6 81.4 1.0
CA 0:CYS46 4.7 75.7 1.0
N 0:CYS16 4.9 82.2 1.0
CE1 0:HIS52 4.9 75.1 1.0
N 0:LYS20 4.9 79.6 1.0
O 0:CYS16 4.9 82.2 1.0

Zinc binding site 4 out of 4 in 8cvm

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Zinc binding site 4 out of 4 in the Cutibacterium Acnes 50S Ribosomal Subunit with P-Site Trna and Sarecycline Bound in the Local Refined Map


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Cutibacterium Acnes 50S Ribosomal Subunit with P-Site Trna and Sarecycline Bound in the Local Refined Map within 5.0Å range:
probe atom residue distance (Å) B Occ
4:Zn101

b:162.0
occ:1.00
 CB 4:CYS41 2.3 146.0 1.0
SG 4:CYS16 2.3 146.2 1.0
N 4:CYS38 2.3 145.4 1.0
SG 4:CYS38 2.3 145.4 1.0
SG 4:CYS18 2.3 148.8 1.0
SG 4:CYS41 2.4 146.0 1.0
CB 4:CYS18 3.0 148.8 1.0
CA 4:VAL37 3.0 143.4 1.0
C 4:VAL37 3.0 143.4 1.0
CA 4:CYS38 3.4 145.4 1.0
CB 4:CYS38 3.5 145.4 1.0
CG2 4:VAL37 3.5 143.4 1.0
O 4:CYS16 3.7 146.2 1.0
CA 4:CYS41 3.7 146.0 1.0
CB 4:VAL37 3.9 143.4 1.0
O 4:CYS41 4.0 146.0 1.0
C 4:CYS41 4.0 146.0 1.0
CB 4:CYS16 4.1 146.2 1.0
N 4:VAL37 4.1 143.4 1.0
O 4:VAL37 4.3 143.4 1.0
C 4:CYS38 4.4 145.4 1.0
N 4:CYS41 4.4 146.0 1.0
O 4:ASP36 4.5 141.2 1.0
CA 4:CYS18 4.5 148.8 1.0
O 4:CYS38 4.5 145.4 1.0
C 4:ASP36 4.6 141.2 1.0
C 4:CYS16 4.7 146.2 1.0
ND2 4:ASN20 4.8 144.4 1.0
N 4:HIS42 4.9 139.6 1.0
O 4:CYS18 4.9 148.8 1.0
CA 4:CYS16 4.9 146.2 1.0
N 4:CYS18 5.0 148.8 1.0

Reference:

I.B.Lomakin, S.C.Devarkar, S.Patel, A.Grada, C.G.Bunick. Sarecycline Inhibits Protein Translation in Cutibacterium Acnes 70S Ribosome Using A Two-Site Mechanism. Nucleic Acids Res. 2023.
ISSN: ESSN 1362-4962
PubMed: 36864821
DOI: 10.1093/NAR/GKAD103
Page generated: Sat Apr 8 08:01:19 2023

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