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Zinc in PDB 4nxm: Crystal Structure of the 30S Ribosomal Subunit From A Gidb (Rsmg) Mutant of Thermus Thermophilus (HB8)

Protein crystallography data

The structure of Crystal Structure of the 30S Ribosomal Subunit From A Gidb (Rsmg) Mutant of Thermus Thermophilus (HB8), PDB code: 4nxm was solved by H.Demirci, F.Murphy Iv, E.Murphy, S.T.Gregory, A.E.Dahlberg, G.Jogl, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 34.62 / 3.65
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 402.923, 402.923, 174.343, 90.00, 90.00, 90.00
R / Rfree (%) 18 / 22.6

Other elements in 4nxm:

The structure of Crystal Structure of the 30S Ribosomal Subunit From A Gidb (Rsmg) Mutant of Thermus Thermophilus (HB8) also contains other interesting chemical elements:

Magnesium (Mg) 224 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of the 30S Ribosomal Subunit From A Gidb (Rsmg) Mutant of Thermus Thermophilus (HB8) (pdb code 4nxm). 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 30S Ribosomal Subunit From A Gidb (Rsmg) Mutant of Thermus Thermophilus (HB8), PDB code: 4nxm:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 4nxm

Go back to Zinc Binding Sites List in 4nxm
Zinc binding site 1 out of 2 in the Crystal Structure of the 30S Ribosomal Subunit From A Gidb (Rsmg) Mutant of Thermus Thermophilus (HB8)


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 30S Ribosomal Subunit From A Gidb (Rsmg) Mutant of Thermus Thermophilus (HB8) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn301

b:79.0
occ:1.00
SG D:CYS31 2.3 0.9 1.0
SG D:CYS26 2.3 0.3 1.0
SG D:CYS9 2.3 0.1 1.0
SG D:CYS12 2.3 0.4 1.0
O D:CYS31 3.4 0.0 1.0
O D:LEU19 3.5 0.3 1.0
CB D:CYS26 3.6 0.8 1.0
CB D:CYS31 3.6 0.7 1.0
CB D:CYS12 3.7 0.7 1.0
CB D:CYS9 3.7 0.5 1.0
CA D:CYS31 4.0 0.4 1.0
CA D:CYS26 4.0 0.1 1.0
CA D:CYS9 4.0 0.9 1.0
C D:CYS31 4.1 0.1 1.0
C D:LEU19 4.7 0.7 1.0
CG D:LYS22 4.9 0.1 1.0
O D:CYS9 4.9 0.5 1.0
N D:CYS26 5.0 0.6 1.0

Zinc binding site 2 out of 2 in 4nxm

Go back to Zinc Binding Sites List in 4nxm
Zinc binding site 2 out of 2 in the Crystal Structure of the 30S Ribosomal Subunit From A Gidb (Rsmg) Mutant of Thermus Thermophilus (HB8)


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 30S Ribosomal Subunit From A Gidb (Rsmg) Mutant of Thermus Thermophilus (HB8) within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Zn101

b:0.6
occ:1.00
SG N:CYS43 2.3 0.8 1.0
SG N:CYS40 2.3 0.3 1.0
SG N:CYS27 2.3 0.9 1.0
SG N:CYS24 2.3 0.3 1.0
CB N:CYS27 2.8 0.6 1.0
CB N:CYS43 3.0 0.8 1.0
CB N:CYS40 3.1 0.2 1.0
N N:CYS27 3.7 0.2 1.0
CB N:ARG29 3.7 0.1 1.0
CB N:CYS24 3.7 0.7 1.0
CA N:CYS27 3.8 0.1 1.0
N N:CYS40 3.9 0.9 1.0
CA N:CYS40 4.1 0.7 1.0
N N:CYS43 4.1 0.9 1.0
CA N:CYS43 4.2 1.0 1.0
CG N:ARG29 4.3 0.6 1.0
N N:ARG29 4.3 1.0 1.0
CD N:ARG29 4.3 0.1 1.0
C N:CYS27 4.4 0.0 1.0
CA N:ARG29 4.5 0.6 1.0
N N:GLY28 4.6 0.3 1.0
C N:CYS40 4.7 0.2 1.0
O N:CYS40 4.7 0.2 1.0
O N:CYS24 4.7 0.2 1.0
O2' A:G1202 4.9 0.0 1.0
C N:ARG26 4.9 0.9 1.0
CA N:CYS24 4.9 0.3 1.0
C N:LEU39 4.9 0.3 1.0
C N:CYS24 5.0 0.7 1.0

Reference:

H.Demirci, F.Murphy Iv, E.Murphy, S.T.Gregory, A.E.Dahlberg, G.Jogl. A Structural Basis For Streptomycin Resistance To Be Published.
Page generated: Wed Dec 16 05:38:02 2020

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