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Zinc in PDB 2hbb: Crystal Structure of the N-Terminal Domain of Ribosomal Protein L9 (NTL9)

Protein crystallography data

The structure of Crystal Structure of the N-Terminal Domain of Ribosomal Protein L9 (NTL9), PDB code: 2hbb was solved by J.-H.Cho, E.Y.Kim, 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 / 1.90
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 53.918, 53.918, 36.339, 90.00, 90.00, 90.00
R / Rfree (%) 19.7 / 23.6

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of the N-Terminal Domain of Ribosomal Protein L9 (NTL9) (pdb code 2hbb). 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 the N-Terminal Domain of Ribosomal Protein L9 (NTL9), PDB code: 2hbb:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 2hbb

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


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

b:20.5
occ:1.00
OD2 A:ASP8 2.0 19.5 1.0
O A:HOH116 2.1 5.1 1.0
O A:HOH105 2.2 9.0 1.0
O A:HOH124 2.3 35.5 1.0
CG A:ASP8 2.8 16.9 1.0
OD1 A:ASP8 3.1 14.7 1.0
O A:HOH111 4.2 18.4 1.0
CB A:ASP8 4.2 15.8 1.0
O A:HOH145 4.3 32.1 1.0
CE A:LYS14 4.8 22.0 1.0
CG A:LYS14 4.9 15.9 1.0

Zinc binding site 2 out of 4 in 2hbb

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Zinc binding site 2 out of 4 in the Crystal Structure of the N-Terminal Domain of Ribosomal Protein L9 (NTL9)


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

b:22.3
occ:1.00
O A:HOH133 2.0 21.9 1.0
OD2 A:ASP23 2.1 19.9 1.0
O A:HOH134 2.4 29.7 1.0
O A:HOH115 2.5 17.9 1.0
O A:HOH132 2.7 36.3 1.0
CG A:ASP23 2.8 12.6 1.0
OD1 A:ASP23 2.9 13.4 1.0
CB A:ASP23 4.2 10.8 1.0
CB A:MET1 4.5 20.1 1.0
N A:MET1 4.5 19.6 1.0
CA A:MET1 4.8 20.3 1.0

Zinc binding site 3 out of 4 in 2hbb

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Zinc binding site 3 out of 4 in the Crystal Structure of the N-Terminal Domain of Ribosomal Protein L9 (NTL9)


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 the N-Terminal Domain of Ribosomal Protein L9 (NTL9) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn103

b:69.5
occ:1.00
OE1 A:GLN50 3.2 46.8 1.0
O A:HOH135 3.3 25.5 0.5
O A:HOH136 3.4 45.2 1.0
O A:HOH151 4.3 40.9 1.0
CD A:GLN50 4.4 44.8 1.0
CD1 A:LEU47 4.8 23.1 1.0
CD1 A:ILE37 4.9 12.3 1.0
NE2 A:GLN50 5.0 45.1 1.0

Zinc binding site 4 out of 4 in 2hbb

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


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 the N-Terminal Domain of Ribosomal Protein L9 (NTL9) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn104

b:64.3
occ:1.00
O A:HOH150 2.6 38.2 1.0
O A:HOH112 2.7 18.8 1.0
O A:HOH145 4.1 32.1 1.0
CD A:LYS15 4.3 18.0 1.0
NZ A:LYS15 4.7 31.8 1.0

Reference:

J.H.Cho, W.Meng, S.Sato, E.Y.Kim, H.Schindelin, D.P.Raleigh. Energetically Significant Networks of Coupled Interactions Within An Unfolded Protein. Proc.Natl.Acad.Sci.Usa V. 111 12079 2014.
ISSN: ISSN 0027-8424
PubMed: 25099351
DOI: 10.1073/PNAS.1402054111
Page generated: Wed Dec 16 03:30:02 2020

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