Zinc in PDB 9c4g: Cutibacterium Acnes 50S Ribosomal Subunit with Clindamycin Bound

Other elements in 9c4g:

The structure of Cutibacterium Acnes 50S Ribosomal Subunit with Clindamycin Bound also contains other interesting chemical elements:

Chlorine (Cl) 1 atom
Magnesium (Mg) 247 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Cutibacterium Acnes 50S Ribosomal Subunit with Clindamycin Bound (pdb code 9c4g). 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 Clindamycin Bound, PDB code: 9c4g:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 9c4g

Go back to Zinc Binding Sites List in 9c4g
Zinc binding site 1 out of 4 in the Cutibacterium Acnes 50S Ribosomal Subunit with Clindamycin Bound


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 Clindamycin Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
w:Zn101

b:64.7
occ:1.00
 SG w:CYS8 2.3 39.3 1.0
SG w:CYS5 2.3 38.4 1.0
SG w:CYS53 2.3 40.2 1.0
SG w:CYS50 2.3 36.2 1.0
O w:ILE7 2.4 48.0 1.0
CB w:CYS5 3.2 33.3 1.0
CB w:CYS8 3.5 39.8 1.0
CB w:CYS53 3.5 36.2 1.0
C w:ILE7 3.5 42.4 1.0
CB w:CYS50 3.6 30.9 1.0
N w:CYS50 3.9 32.6 1.0
CA w:CYS50 4.3 29.8 1.0
N w:CYS8 4.3 38.6 1.0
CA w:CYS8 4.4 38.8 1.0
N w:CYS53 4.4 32.9 1.0
CA w:ILE7 4.5 39.1 1.0
CB w:LYS10 4.5 32.7 1.0
CA w:CYS53 4.6 34.8 1.0
CB w:ILE7 4.6 38.8 1.0
CG2 w:ILE7 4.6 40.9 1.0
CA w:CYS5 4.6 34.0 1.0
CE w:LYS10 4.7 26.2 1.0
C w:CYS8 4.8 39.3 1.0
N w:ILE7 4.8 40.4 1.0
O w:CYS50 4.9 31.8 1.0
C w:CYS50 5.0 30.6 1.0
N w:ALA9 5.0 39.0 1.0
N w:LYS10 5.0 36.2 1.0

Zinc binding site 2 out of 4 in 9c4g

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Zinc binding site 2 out of 4 in the Cutibacterium Acnes 50S Ribosomal Subunit with Clindamycin Bound


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 Clindamycin Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
z:Zn101

b:83.9
occ:1.00
 SG z:CYS48 2.3 56.8 1.0
SG z:CYS45 2.3 55.5 1.0
SG z:CYS30 2.3 56.1 1.0
SG z:CYS35 2.3 61.4 1.0
CB z:CYS45 3.0 44.4 1.0
CB z:CYS35 3.1 61.8 1.0
CB z:CYS30 3.1 51.3 1.0
CB z:CYS48 3.6 53.1 1.0
N z:CYS48 3.9 52.4 1.0
CA z:CYS48 4.4 54.3 1.0
NH2 z:ARG57 4.4 49.8 1.0
CA z:CYS45 4.5 42.6 1.0
CA z:CYS35 4.5 63.4 1.0
CA z:CYS30 4.5 48.5 1.0
CB z:SER47 4.5 55.6 1.0
O z:GLU37 4.6 50.1 1.0
N z:GLU37 4.7 57.3 1.0
CB z:GLU37 4.7 53.1 1.0
C z:SER47 4.8 53.6 1.0
CB z:ASN32 4.8 58.6 1.0
C z:CYS35 4.9 61.3 1.0
N z:GLY36 4.9 58.8 1.0
N z:SER47 4.9 52.0 1.0
C z:CYS45 5.0 45.6 1.0
CA z:SER47 5.0 53.0 1.0

Zinc binding site 3 out of 4 in 9c4g

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Zinc binding site 3 out of 4 in the Cutibacterium Acnes 50S Ribosomal Subunit with Clindamycin Bound


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 Clindamycin Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
0:Zn101

b:68.2
occ:1.00
 SG 0:CYS16 2.2 48.8 1.0
CB 0:CYS16 2.2 35.9 1.0
SG 0:CYS19 2.3 42.6 1.0
SG 0:CYS43 2.3 34.8 1.0
SG 0:CYS46 2.4 50.0 1.0
CB 0:CYS43 3.3 29.9 1.0
CA 0:CYS16 3.7 32.5 1.0
N 0:CYS19 3.8 39.9 1.0
CB 0:CYS19 3.8 43.3 1.0
OG1 0:THR50 4.0 38.5 1.0
CB 0:CYS46 4.0 41.5 1.0
ND2 0:ASN23 4.3 32.6 1.0
CA 0:CYS19 4.3 42.5 1.0
CB 0:GLU18 4.4 44.1 1.0
C 0:CYS16 4.4 40.0 1.0
N 0:CYS16 4.5 30.8 1.0
CB 0:GLU21 4.5 38.1 1.0
N 0:GLU18 4.6 43.1 1.0
N 0:CYS46 4.6 40.5 1.0
CA 0:CYS43 4.7 29.6 1.0
CG2 0:THR50 4.8 35.2 1.0
C 0:GLU18 4.8 44.0 1.0
CA 0:GLU18 4.8 44.2 1.0
N 0:GLU21 4.9 40.2 1.0
C 0:CYS19 4.9 43.7 1.0
N 0:LYS20 4.9 41.2 1.0
CB 0:THR50 4.9 34.2 1.0
O 0:CYS16 4.9 39.8 1.0
CE1 0:HIS52 5.0 29.4 1.0

Zinc binding site 4 out of 4 in 9c4g

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Zinc binding site 4 out of 4 in the Cutibacterium Acnes 50S Ribosomal Subunit with Clindamycin Bound


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 Clindamycin Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
4:Zn101

b:15.8
occ:1.00
 CB 4:CYS41 2.0 14.8 1.0
SG 4:CYS16 2.3 1.2 1.0
SG 4:CYS18 2.3 13.9 1.0
SG 4:CYS38 2.3 2.7 1.0
SG 4:CYS41 2.4 10.7 1.0
N 4:CYS38 2.4 3.4 1.0
CA 4:VAL37 3.1 8.8 1.0
C 4:VAL37 3.2 6.8 1.0
CA 4:CYS38 3.4 8.0 1.0
O 4:CYS16 3.4 5.5 1.0
CB 4:CYS38 3.4 6.6 1.0
CG2 4:VAL37 3.4 6.8 1.0
CA 4:CYS41 3.5 17.2 1.0
CB 4:CYS18 3.7 18.1 1.0
CB 4:VAL37 3.9 9.3 1.0
CB 4:CYS16 3.9 8.4 1.0
O 4:CYS38 4.1 9.0 1.0
C 4:CYS38 4.1 8.8 1.0
N 4:CYS41 4.1 10.9 1.0
C 4:CYS41 4.2 17.9 1.0
N 4:VAL37 4.3 5.7 1.0
C 4:CYS16 4.3 5.4 1.0
O 4:VAL37 4.3 12.3 1.0
ND2 4:ASN20 4.5 12.7 1.0
O 4:ASP36 4.5 16.8 1.0
CA 4:CYS16 4.6 8.6 1.0
O 4:CYS41 4.6 16.0 1.0
N 4:CYS18 4.8 20.6 1.0
CA 4:CYS18 4.9 16.4 1.0
C 4:ASP36 4.9 13.3 1.0
N 4:HIS42 4.9 15.6 1.0

Reference:

I.B.Lomakin, S.C.Devarkar, A.Grada, C.G.Bunick. Mechanistic Basis For the Translation Inhibition of Cutibacterium Acnes By Clindamycin. J Invest Dermatol. 2024.
ISSN: ESSN 1523-1747
PubMed: 39122144
DOI: 10.1016/J.JID.2024.07.013
Page generated: Thu Oct 31 14:48:34 2024

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