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Zinc in PDB 4ox9: Crystal Structure of the Aminoglycoside Resistance Methyltransferase Npma Bound to the 30S Ribosomal Subunit

Enzymatic activity of Crystal Structure of the Aminoglycoside Resistance Methyltransferase Npma Bound to the 30S Ribosomal Subunit

All present enzymatic activity of Crystal Structure of the Aminoglycoside Resistance Methyltransferase Npma Bound to the 30S Ribosomal Subunit:
2.1.1.180;

Protein crystallography data

The structure of Crystal Structure of the Aminoglycoside Resistance Methyltransferase Npma Bound to the 30S Ribosomal Subunit, PDB code: 4ox9 was solved by J.A.Dunkle, G.L.Conn, C.M.Dunham, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.72 / 3.80
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 403.520, 403.520, 176.610, 90.00, 90.00, 90.00
R / Rfree (%) 23.3 / 25.7

Other elements in 4ox9:

The structure of Crystal Structure of the Aminoglycoside Resistance Methyltransferase Npma Bound to the 30S Ribosomal Subunit also contains other interesting chemical elements:

Magnesium (Mg) 120 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of the Aminoglycoside Resistance Methyltransferase Npma Bound to the 30S Ribosomal Subunit (pdb code 4ox9). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Crystal Structure of the Aminoglycoside Resistance Methyltransferase Npma Bound to the 30S Ribosomal Subunit, PDB code: 4ox9:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 4ox9

Go back to Zinc Binding Sites List in 4ox9
Zinc binding site 1 out of 2 in the Crystal Structure of the Aminoglycoside Resistance Methyltransferase Npma Bound to the 30S Ribosomal Subunit


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of the Aminoglycoside Resistance Methyltransferase Npma Bound to the 30S Ribosomal Subunit within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn301

b:34.5
occ:1.00
 SG D:CYS31 2.3 85.6 1.0
SG D:CYS9 2.6 91.1 1.0
SG D:CYS26 2.7 0.0 1.0
SG D:CYS12 2.9 84.5 1.0
O D:CYS31 3.2 85.6 1.0
CB D:CYS31 3.5 85.6 1.0
CA D:CYS31 3.6 85.6 1.0
O D:LEU19 3.7 0.0 1.0
C D:CYS31 3.8 85.6 1.0
CB D:CYS9 3.9 91.1 1.0
CB D:CYS12 4.2 84.5 1.0
CA D:CYS9 4.2 91.1 1.0
CB D:CYS26 4.2 0.0 1.0
CA D:CYS26 4.6 0.0 1.0
C D:LEU19 4.9 0.0 1.0
N D:CYS31 5.0 85.6 1.0

Zinc binding site 2 out of 2 in 4ox9

Go back to Zinc Binding Sites List in 4ox9
Zinc binding site 2 out of 2 in the Crystal Structure of the Aminoglycoside Resistance Methyltransferase Npma Bound to the 30S Ribosomal Subunit


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of the Aminoglycoside Resistance Methyltransferase Npma Bound to the 30S Ribosomal Subunit within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Zn101

b:0.3
occ:1.00
 SG N:CYS27 2.0 44.1 1.0
SG N:CYS43 2.2 71.3 1.0
SG N:CYS24 2.4 79.1 1.0
SG N:CYS40 2.4 80.5 1.0
CB N:CYS27 3.2 44.1 1.0
CB N:CYS43 3.3 71.3 1.0
CB N:CYS24 3.5 79.1 1.0
CB N:CYS40 3.5 80.5 1.0
N N:CYS27 3.8 44.1 1.0
N N:CYS40 3.9 80.5 1.0
CB N:ARG29 4.0 0.3 1.0
CA N:CYS27 4.1 44.1 1.0
N N:CYS43 4.2 71.3 1.0
CA N:CYS40 4.3 80.5 1.0
CA N:CYS43 4.3 71.3 1.0
CB N:ARG26 4.6 87.5 1.0
C N:ARG26 4.6 87.5 1.0
N N:ARG29 4.7 0.3 1.0
N2 A:G1202 4.7 87.1 1.0
O N:CYS40 4.7 80.5 1.0
C N:CYS27 4.7 44.1 1.0
N N:GLY28 4.8 0.6 1.0
CD2 N:LEU39 4.8 0.8 1.0
C N:CYS40 4.9 80.5 1.0
CA N:CYS24 4.9 79.1 1.0
CG N:ARG26 4.9 87.5 1.0
CA N:ARG26 5.0 87.5 1.0

Reference:

J.A.Dunkle, K.Vinal, P.M.Desai, N.Zelinskaya, M.Savic, D.M.West, G.L.Conn, C.M.Dunham. Molecular Recognition and Modification of the 30S Ribosome By the Aminoglycoside-Resistance Methyltransferase Npma. Proc.Natl.Acad.Sci.Usa V. 111 6275 2014.
ISSN: ESSN 1091-6490
PubMed: 24717845
DOI: 10.1073/PNAS.1402789111
Page generated: Sun Oct 27 04:06:26 2024

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