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Zinc in PDB 1v13: Crystal Structure of the Mutant HIS103ALA of the Colicin E9 Dnase Domain in Complex with Zn+2 (2.0 Angstroms)

Protein crystallography data

The structure of Crystal Structure of the Mutant HIS103ALA of the Colicin E9 Dnase Domain in Complex with Zn+2 (2.0 Angstroms), PDB code: 1v13 was solved by M.J.Mate, C.Kleanthous, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.64 / 2.00
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 52.693, 61.441, 91.107, 90.00, 90.00, 90.00
R / Rfree (%) 23 / 30.7

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of the Mutant HIS103ALA of the Colicin E9 Dnase Domain in Complex with Zn+2 (2.0 Angstroms) (pdb code 1v13). 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 Mutant HIS103ALA of the Colicin E9 Dnase Domain in Complex with Zn+2 (2.0 Angstroms), PDB code: 1v13:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 1v13

Go back to Zinc Binding Sites List in 1v13
Zinc binding site 1 out of 2 in the Crystal Structure of the Mutant HIS103ALA of the Colicin E9 Dnase Domain in Complex with Zn+2 (2.0 Angstroms)


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 Mutant HIS103ALA of the Colicin E9 Dnase Domain in Complex with Zn+2 (2.0 Angstroms) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn200

b:48.5
occ:1.00
O A:HOH2027 1.4 32.6 1.0
NE2 A:HIS131 1.9 52.5 1.0
ND1 A:HIS102 1.9 50.0 1.0
NE2 A:HIS127 2.2 50.7 1.0
CE1 A:HIS102 2.7 53.4 1.0
CE1 A:HIS131 2.9 53.2 1.0
CD2 A:HIS131 2.9 53.1 1.0
CD2 A:HIS127 2.9 46.5 1.0
CG A:HIS102 3.2 53.7 1.0
O A:HOH2028 3.3 39.4 1.0
O A:HOH2026 3.3 38.5 1.0
CE1 A:HIS127 3.3 46.0 1.0
CB A:HIS102 3.7 52.8 1.0
NE2 A:HIS102 3.9 50.6 1.0
CA A:HIS102 3.9 52.8 1.0
ND1 A:HIS131 4.0 50.3 1.0
CG A:HIS131 4.0 49.9 1.0
N A:ALA103 4.1 54.0 1.0
CD2 A:HIS102 4.1 49.6 1.0
CG A:HIS127 4.2 48.5 1.0
ND1 A:HIS127 4.3 46.8 1.0
CB B:HIS131 4.4 50.5 1.0
C A:HIS102 4.4 53.1 1.0
O A:ALA103 4.5 54.4 1.0
CG B:HIS131 4.6 49.0 1.0
O B:HOH2044 4.6 37.4 1.0
CD2 B:HIS131 4.9 44.2 1.0
O A:HOH2018 4.9 38.6 1.0
O A:HIS127 5.0 51.1 1.0

Zinc binding site 2 out of 2 in 1v13

Go back to Zinc Binding Sites List in 1v13
Zinc binding site 2 out of 2 in the Crystal Structure of the Mutant HIS103ALA of the Colicin E9 Dnase Domain in Complex with Zn+2 (2.0 Angstroms)


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 Mutant HIS103ALA of the Colicin E9 Dnase Domain in Complex with Zn+2 (2.0 Angstroms) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn200

b:38.7
occ:1.00
O B:HOH2064 2.0 35.6 1.0
NE2 B:HIS131 2.0 44.3 1.0
ND1 B:HIS102 2.0 46.4 1.0
NE2 B:HIS127 2.0 48.9 1.0
CE1 B:HIS102 2.9 45.2 1.0
CD2 B:HIS127 3.0 48.0 1.0
CE1 B:HIS131 3.0 45.2 1.0
O B:HOH2065 3.0 31.7 1.0
CD2 B:HIS131 3.1 44.2 1.0
CE1 B:HIS127 3.1 48.4 1.0
CG B:HIS102 3.1 46.1 1.0
CB B:HIS102 3.6 46.4 1.0
CA B:HIS102 3.7 47.3 1.0
N B:ALA103 3.8 48.6 1.0
NE2 B:HIS102 4.0 46.4 1.0
ND1 B:HIS131 4.1 46.2 1.0
CG B:HIS127 4.1 47.3 1.0
O B:ALA103 4.2 48.8 1.0
ND1 B:HIS127 4.2 43.2 1.0
CG B:HIS131 4.2 49.0 1.0
CD2 B:HIS102 4.2 48.3 1.0
O B:HOH2035 4.2 39.2 1.0
C B:HIS102 4.2 46.8 1.0
CB A:HIS131 4.3 49.2 1.0
CG A:HIS131 4.6 49.9 1.0
C B:ALA103 4.7 48.5 1.0
O B:HOH2054 4.7 50.1 1.0
O A:HOH2018 4.8 38.6 1.0
CA B:ALA103 4.8 48.2 1.0
CD2 A:HIS131 5.0 53.1 1.0

Reference:

M.J.Mate, C.Kleanthous. Structure-Based Analysis of the Metal-Dependent Mechanism of H-N-H Endonucleases J.Biol.Chem. V. 279 34763 2004.
ISSN: ISSN 0021-9258
PubMed: 15190054
DOI: 10.1074/JBC.M403719200
Page generated: Mon Jan 25 16:14:51 2021

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