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Zinc in PDB 2gyk: Crystal Structure of the Complex of the Colicin E9 Dnase Domain with A Mutant Immunity Protein, IMME9 (D51A)

Enzymatic activity of Crystal Structure of the Complex of the Colicin E9 Dnase Domain with A Mutant Immunity Protein, IMME9 (D51A)

All present enzymatic activity of Crystal Structure of the Complex of the Colicin E9 Dnase Domain with A Mutant Immunity Protein, IMME9 (D51A):
3.1.21.1;

Protein crystallography data

The structure of Crystal Structure of the Complex of the Colicin E9 Dnase Domain with A Mutant Immunity Protein, IMME9 (D51A), PDB code: 2gyk was solved by P.S.Santi, O.O.Kolade, U.C.Kuhlmann, A.M.Hemmings, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.86 / 1.60
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 44.903, 88.248, 52.235, 90.00, 91.92, 90.00
R / Rfree (%) 18.5 / 23.2

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of the Complex of the Colicin E9 Dnase Domain with A Mutant Immunity Protein, IMME9 (D51A) (pdb code 2gyk). 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 Complex of the Colicin E9 Dnase Domain with A Mutant Immunity Protein, IMME9 (D51A), PDB code: 2gyk:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 2gyk

Go back to Zinc Binding Sites List in 2gyk
Zinc binding site 1 out of 2 in the Crystal Structure of the Complex of the Colicin E9 Dnase Domain with A Mutant Immunity Protein, IMME9 (D51A)


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 Complex of the Colicin E9 Dnase Domain with A Mutant Immunity Protein, IMME9 (D51A) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn301

b:12.9
occ:1.00
O3 B:PO4703 1.8 17.0 1.0
ND1 B:HIS102 2.1 8.0 1.0
NE2 B:HIS127 2.1 10.0 1.0
NE2 B:HIS131 2.1 8.3 1.0
CE1 B:HIS102 3.0 5.8 1.0
CD2 B:HIS127 3.0 10.5 1.0
CD2 B:HIS131 3.0 10.7 1.0
CE1 B:HIS131 3.1 10.3 1.0
P B:PO4703 3.1 18.1 1.0
CE1 B:HIS127 3.1 10.7 1.0
CG B:HIS102 3.1 6.2 1.0
O1 B:PO4703 3.4 27.9 1.0
CB B:HIS102 3.5 7.0 1.0
CA B:HIS102 3.7 6.9 1.0
O2 B:PO4703 3.7 26.3 1.0
O B:HOH716 3.9 17.2 1.0
N B:HIS103 4.0 6.2 1.0
NE2 B:HIS102 4.1 6.8 1.0
CG B:HIS127 4.2 10.5 1.0
ND1 B:HIS127 4.2 9.9 1.0
ND1 B:HIS131 4.2 12.6 1.0
CG B:HIS131 4.2 12.6 1.0
CD2 B:HIS102 4.2 7.0 1.0
O4 B:PO4703 4.3 21.1 1.0
C B:HIS102 4.3 6.8 1.0
O B:HIS103 4.5 5.4 1.0
O B:LEU101 4.8 9.7 1.0
N B:HIS102 4.9 7.4 1.0

Zinc binding site 2 out of 2 in 2gyk

Go back to Zinc Binding Sites List in 2gyk
Zinc binding site 2 out of 2 in the Crystal Structure of the Complex of the Colicin E9 Dnase Domain with A Mutant Immunity Protein, IMME9 (D51A)


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 Complex of the Colicin E9 Dnase Domain with A Mutant Immunity Protein, IMME9 (D51A) within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn301

b:21.8
occ:1.00
O2 F:PO4704 1.9 21.9 1.0
ND1 F:HIS102 2.1 13.0 1.0
NE2 F:HIS131 2.1 22.6 1.0
NE2 F:HIS127 2.1 14.2 1.0
CE1 F:HIS102 2.9 10.7 1.0
CD2 F:HIS127 3.0 16.3 1.0
CD2 F:HIS131 3.0 24.8 1.0
P F:PO4704 3.1 24.2 1.0
CE1 F:HIS131 3.1 25.7 1.0
CG F:HIS102 3.1 10.8 1.0
CE1 F:HIS127 3.2 16.1 1.0
O4 F:PO4704 3.4 28.4 1.0
O1 F:PO4704 3.5 26.3 1.0
CB F:HIS102 3.6 9.7 1.0
CA F:HIS102 3.7 8.9 1.0
O F:HOH759 3.9 30.6 1.0
N F:HIS103 4.0 8.0 1.0
NE2 F:HIS102 4.1 14.2 1.0
CG F:HIS127 4.2 15.7 1.0
CG F:HIS131 4.2 25.4 1.0
CD2 F:HIS102 4.2 11.5 1.0
ND1 F:HIS131 4.2 25.1 1.0
ND1 F:HIS127 4.3 15.0 1.0
O F:HIS103 4.3 8.4 1.0
C F:HIS102 4.3 8.9 1.0
O3 F:PO4704 4.4 23.5 1.0

Reference:

U.C.Kuhlmann, P.S.Santi, O.O.Kolade, G.R.Moore, R.James, C.Kleanthous, A.M.Hemmings. Crystal Structures of the Complexes of the Colicin E9 Dnase Domain with Mutant Immunity Proteins To Be Published.
Page generated: Wed Dec 16 03:29:40 2020

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