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Zinc in PDB 7y41: Mycobacterium Smegmatis 50S Ribosomal Subunit From Log Phase of Growth

Other elements in 7y41:

The structure of Mycobacterium Smegmatis 50S Ribosomal Subunit From Log Phase of Growth also contains other interesting chemical elements:

Magnesium (Mg) 407 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Mycobacterium Smegmatis 50S Ribosomal Subunit From Log Phase of Growth (pdb code 7y41). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Mycobacterium Smegmatis 50S Ribosomal Subunit From Log Phase of Growth, PDB code: 7y41:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 7y41

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Zinc binding site 1 out of 4 in the Mycobacterium Smegmatis 50S Ribosomal Subunit From Log Phase of Growth


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Mycobacterium Smegmatis 50S Ribosomal Subunit From Log Phase of Growth within 5.0Å range:
probe atom residue distance (Å) B Occ
Y:Zn101

b:147.6
occ:1.00
 SG Y:CYS52 2.3 119.2 1.0
SG Y:CYS55 2.3 121.1 1.0
SG Y:CYS8 2.3 122.3 1.0
SG Y:CYS5 2.3 116.2 1.0
CB Y:CYS8 3.2 122.3 1.0
CB Y:CYS5 3.2 116.2 1.0
CB Y:CYS52 3.4 119.2 1.0
CB Y:CYS55 3.4 121.1 1.0
N Y:CYS8 3.5 122.3 1.0
N Y:CYS52 3.7 119.2 1.0
CA Y:CYS8 3.9 122.3 1.0
CA Y:CYS52 4.1 119.2 1.0
N Y:CYS55 4.3 121.1 1.0
CA Y:CYS55 4.4 121.1 1.0
CB Y:ILE7 4.4 118.6 1.0
O Y:CYS52 4.5 119.2 1.0
C Y:ILE7 4.6 118.6 1.0
C Y:CYS8 4.6 122.3 1.0
CA Y:CYS5 4.7 116.2 1.0
C Y:CYS52 4.7 119.2 1.0
N Y:GLY9 4.8 119.6 1.0
N Y:ILE7 4.8 118.6 1.0
CB Y:LYS10 4.8 116.8 1.0
NZ Y:LYS60 4.9 120.4 1.0
C Y:ALA51 4.9 117.8 1.0
CA Y:ILE7 4.9 118.6 1.0

Zinc binding site 2 out of 4 in 7y41

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Zinc binding site 2 out of 4 in the Mycobacterium Smegmatis 50S Ribosomal Subunit From Log Phase of Growth


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Mycobacterium Smegmatis 50S Ribosomal Subunit From Log Phase of Growth within 5.0Å range:
probe atom residue distance (Å) B Occ
c:Zn101

b:206.1
occ:1.00
 SG c:CYS42 2.3 174.4 1.0
SG c:CYS18 2.3 196.6 1.0
SG c:CYS15 2.3 188.0 1.0
SG c:CYS45 2.3 178.5 1.0
CB c:CYS15 2.9 188.0 1.0
NE2 c:GLN49 3.1 172.6 1.0
OD1 c:ASN44 3.1 181.1 1.0
CB c:CYS18 3.3 196.6 1.0
CB c:CYS45 3.4 178.5 1.0
N c:CYS18 3.5 196.6 1.0
CB c:CYS42 3.5 174.4 1.0
CA c:CYS18 4.0 196.6 1.0
N c:CYS45 4.2 178.5 1.0
CG c:ASN44 4.2 181.1 1.0
CD c:GLN49 4.3 172.6 1.0
CB c:VAL17 4.4 194.1 1.0
CA c:CYS15 4.4 188.0 1.0
CA c:CYS45 4.4 178.5 1.0
ND2 c:ASN44 4.6 181.1 1.0
C c:VAL17 4.6 194.1 1.0
N c:VAL17 4.7 194.1 1.0
N c:LYS19 4.7 191.4 1.0
ND2 c:ASN22 4.7 166.8 1.0
C c:CYS18 4.7 196.6 1.0
OE1 c:GLN49 4.7 172.6 1.0
CA c:VAL17 4.8 194.1 1.0
CA c:CYS42 4.9 174.4 1.0
C c:CYS15 5.0 188.0 1.0

Zinc binding site 3 out of 4 in 7y41

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Zinc binding site 3 out of 4 in the Mycobacterium Smegmatis 50S Ribosomal Subunit From Log Phase of Growth


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Mycobacterium Smegmatis 50S Ribosomal Subunit From Log Phase of Growth within 5.0Å range:
probe atom residue distance (Å) B Occ
f:Zn101

b:160.8
occ:1.00
 ND1 f:HIS32 2.0 131.1 1.0
SG f:CYS11 2.3 141.7 1.0
SG f:CYS27 2.3 138.3 1.0
SG f:CYS14 2.3 144.1 1.0
CG f:HIS32 2.9 131.1 1.0
CB f:CYS27 3.0 138.3 1.0
CE1 f:HIS32 3.1 131.1 1.0
CB f:HIS32 3.1 131.1 1.0
N f:CYS14 3.7 144.1 1.0
CB f:CYS14 3.7 144.1 1.0
CB f:CYS11 3.9 141.7 1.0
CA f:CYS14 3.9 144.1 1.0
O f:CYS11 4.0 141.7 1.0
N f:CYS11 4.1 141.7 1.0
CD2 f:HIS32 4.1 131.1 1.0
NE2 f:HIS32 4.2 131.1 1.0
C f:LYS13 4.3 147.4 1.0
CA f:CYS11 4.3 141.7 1.0
C f:CYS11 4.5 141.7 1.0
CA f:CYS27 4.5 138.3 1.0
CB f:LYS13 4.6 147.4 1.0
CA f:HIS32 4.6 131.1 1.0
CB f:ASP29 4.7 132.5 1.0
CA f:LYS13 4.8 147.4 1.0
O f:LYS13 4.9 147.4 1.0
N f:LYS13 4.9 147.4 1.0

Zinc binding site 4 out of 4 in 7y41

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Zinc binding site 4 out of 4 in the Mycobacterium Smegmatis 50S Ribosomal Subunit From Log Phase of Growth


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Mycobacterium Smegmatis 50S Ribosomal Subunit From Log Phase of Growth within 5.0Å range:
probe atom residue distance (Å) B Occ
g:Zn101

b:360.7
occ:1.00
 SG g:CYS41 2.3 320.9 1.0
SG g:CYS16 2.3 336.5 1.0
SG g:CYS18 2.3 334.4 1.0
SG g:CYS38 2.3 316.5 1.0
CB g:CYS18 2.8 334.4 1.0
CB g:CYS38 3.3 316.5 1.0
CB g:CYS16 3.3 336.5 1.0
CB g:CYS41 3.4 320.9 1.0
N g:CYS18 3.8 334.4 1.0
CA g:CYS18 3.9 334.4 1.0
N g:CYS41 3.9 320.9 1.0
N g:CYS38 4.1 316.5 1.0
CA g:CYS41 4.2 320.9 1.0
CA g:CYS38 4.3 316.5 1.0
CB g:HIS20 4.6 323.5 1.0
CA g:CYS16 4.7 336.5 1.0
C g:CYS18 4.7 334.4 1.0
N g:GLY17 4.8 333.2 1.0
C g:CYS16 4.8 336.5 1.0
O g:GLU36 4.9 322.5 1.0
C g:GLN40 4.9 313.2 1.0
CB g:GLN40 4.9 313.2 1.0
C g:CYS38 5.0 316.5 1.0
C g:GLY17 5.0 333.2 1.0
N g:GLN40 5.0 313.2 1.0

Reference:

J.Sengupta, P.Baid. Cryo-Em Structures Reveal A Unique Conformational Dynamics of the Mycobacterium 23S Rrna Helices To Be Published.
Page generated: Fri Aug 22 06:55:35 2025

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