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Zinc in PDB 2hvf: Crystal Structure of N-Terminal Domain of Ribosomal Protein L9 (NTL9), G34DA

Protein crystallography data

The structure of Crystal Structure of N-Terminal Domain of Ribosomal Protein L9 (NTL9), G34DA, PDB code: 2hvf was solved by B.Anil, E.Y.Kim, J.H.Cho, H.Schindelin, D.P.Raleigh, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 1.57
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 53.517, 53.517, 36.178, 90.00, 90.00, 90.00
R / Rfree (%) 15.9 / 20.8

Other elements in 2hvf:

The structure of Crystal Structure of N-Terminal Domain of Ribosomal Protein L9 (NTL9), G34DA also contains other interesting chemical elements:

Chlorine (Cl) 5 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of N-Terminal Domain of Ribosomal Protein L9 (NTL9), G34DA (pdb code 2hvf). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Crystal Structure of N-Terminal Domain of Ribosomal Protein L9 (NTL9), G34DA, PDB code: 2hvf:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 2hvf

Go back to Zinc Binding Sites List in 2hvf
Zinc binding site 1 out of 4 in the Crystal Structure of N-Terminal Domain of Ribosomal Protein L9 (NTL9), G34DA


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 N-Terminal Domain of Ribosomal Protein L9 (NTL9), G34DA within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn101

b:19.4
occ:1.00
OD2 A:ASP8 1.9 17.0 1.0
O A:HOH447 1.9 30.1 1.0
CL A:CL204 2.1 16.1 0.5
CL A:CL203 2.2 21.8 1.0
CL A:CL204 2.4 20.5 0.5
CG A:ASP8 2.8 14.1 1.0
OD1 A:ASP8 3.1 14.1 1.0
O A:HOH461 3.8 44.1 1.0
CB A:ASP8 4.2 14.1 1.0
CG A:LYS14 4.8 16.0 1.0
CE A:LYS14 4.9 20.2 1.0

Zinc binding site 2 out of 4 in 2hvf

Go back to Zinc Binding Sites List in 2hvf
Zinc binding site 2 out of 4 in the Crystal Structure of N-Terminal Domain of Ribosomal Protein L9 (NTL9), G34DA


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 N-Terminal Domain of Ribosomal Protein L9 (NTL9), G34DA within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn102

b:18.3
occ:1.00
OD2 A:ASP23 2.0 18.1 1.0
CL A:CL202 2.1 35.2 1.0
O A:HOH432 2.3 31.2 1.0
O A:HOH427 2.4 30.5 1.0
O A:HOH411 2.4 13.7 1.0
CG A:ASP23 2.8 12.1 1.0
OD1 A:ASP23 2.9 14.3 1.0
O A:HOH460 4.0 35.2 1.0
O A:HOH459 4.2 41.2 1.0
CB A:ASP23 4.2 10.8 1.0
N A:MET1 4.5 14.7 1.0
CB A:MET1 4.6 19.3 1.0
CA A:MET1 4.8 17.0 1.0

Zinc binding site 3 out of 4 in 2hvf

Go back to Zinc Binding Sites List in 2hvf
Zinc binding site 3 out of 4 in the Crystal Structure of N-Terminal Domain of Ribosomal Protein L9 (NTL9), G34DA


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of N-Terminal Domain of Ribosomal Protein L9 (NTL9), G34DA within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn103

b:21.3
occ:0.50
O A:HOH414 1.8 16.7 0.4
N1 A:IMD301 2.0 25.9 0.5
O A:HOH414 2.4 16.4 0.6
NE2 A:GLN50 2.6 40.7 1.0
C5 A:IMD301 2.7 26.5 0.5
C2 A:IMD301 3.1 25.9 0.5
CD A:GLN50 3.4 35.7 1.0
OE1 A:GLN50 3.4 40.6 1.0
C4 A:IMD301 4.0 26.1 0.5
N3 A:IMD301 4.1 25.8 0.5
O A:HOH463 4.5 48.9 1.0
CG A:GLN50 4.8 34.3 1.0
CD1 A:ILE37 4.9 12.3 1.0

Zinc binding site 4 out of 4 in 2hvf

Go back to Zinc Binding Sites List in 2hvf
Zinc binding site 4 out of 4 in the Crystal Structure of N-Terminal Domain of Ribosomal Protein L9 (NTL9), G34DA


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of N-Terminal Domain of Ribosomal Protein L9 (NTL9), G34DA within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn104

b:31.3
occ:1.00
OE1 A:GLU17 2.0 18.3 1.0
CL A:CL201 2.2 32.1 1.0
O A:HOH464 2.2 21.7 1.0
CD A:GLU17 2.8 14.7 1.0
OE2 A:GLU17 2.8 17.4 1.0
O A:HOH422 3.5 39.2 1.0
NZ A:LYS19 3.8 25.0 1.0
CD A:LYS14 4.1 17.2 1.0
CG A:GLU17 4.2 13.9 1.0
CG A:LYS14 4.3 16.0 1.0
O A:HOH418 4.6 15.9 0.5
CB A:LYS14 4.7 14.1 1.0
N A:LYS14 4.8 13.5 1.0
CE A:LYS14 4.9 20.2 1.0
CE A:LYS19 4.9 24.5 1.0

Reference:

B.Anil, E.Y.Kim, J.H.Cho, H.Schindelin, D.P.Raleigh. Detecting and Quantifying Strain in Protein Folding To Be Published.
Page generated: Wed Dec 16 03:30:27 2020

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