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Zinc in PDB 3u43: Crystal Structure of the Colicin E2 Dnase-IM2 Complex

Protein crystallography data

The structure of Crystal Structure of the Colicin E2 Dnase-IM2 Complex, PDB code: 3u43 was solved by J.A.Wojdyla, C.Kleanthous, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.81 / 1.72
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 121.814, 53.277, 32.785, 90.00, 90.00, 90.00
R / Rfree (%) 16.2 / 20.3

Other elements in 3u43:

The structure of Crystal Structure of the Colicin E2 Dnase-IM2 Complex also contains other interesting chemical elements:

Calcium (Ca) 1 atom

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of the Colicin E2 Dnase-IM2 Complex (pdb code 3u43). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total only one binding site of Zinc was determined in the Crystal Structure of the Colicin E2 Dnase-IM2 Complex, PDB code: 3u43:

Zinc binding site 1 out of 1 in 3u43

Go back to Zinc Binding Sites List in 3u43
Zinc binding site 1 out of 1 in the Crystal Structure of the Colicin E2 Dnase-IM2 Complex


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 Colicin E2 Dnase-IM2 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn135

b:17.6
occ:1.00
O B:HOH386 2.0 15.8 1.0
NE2 B:HIS127 2.1 12.7 1.0
ND1 B:HIS102 2.1 10.8 1.0
NE2 B:HIS131 2.2 14.7 1.0
O B:HOH385 2.3 13.6 1.0
O B:HOH388 2.3 17.2 1.0
CE1 B:HIS102 2.9 11.4 1.0
O B:HOH393 3.0 30.1 1.0
CD2 B:HIS127 3.0 12.7 1.0
CE1 B:HIS131 3.1 18.2 1.0
CE1 B:HIS127 3.2 16.4 1.0
CD2 B:HIS131 3.3 16.1 1.0
CG B:HIS102 3.3 11.3 1.0
CB B:HIS102 3.8 11.0 1.0
N B:HIS103 3.9 11.0 1.0
CA B:HIS102 4.0 11.2 1.0
O B:HOH390 4.0 18.2 1.0
O B:HOH389 4.1 15.2 1.0
NE2 B:HIS102 4.1 12.7 1.0
CG B:HIS127 4.2 12.2 1.0
O B:HIS103 4.2 10.6 1.0
ND1 B:HIS127 4.2 15.3 1.0
ND1 B:HIS131 4.3 18.1 1.0
CD2 B:HIS102 4.3 9.9 1.0
CG B:HIS131 4.4 17.5 1.0
O B:HOH391 4.4 29.4 1.0
C B:HIS102 4.4 11.7 1.0
C B:HIS103 4.8 10.2 1.0
CA B:HIS103 4.8 10.1 1.0

Reference:

J.A.Wojdyla, S.J.Fleishman, D.Baker, C.Kleanthous. Structure of the Ultra-High-Affinity Colicin E2 Dnase-IM2 Complex. J.Mol.Biol. V. 417 79 2012.
ISSN: ISSN 0022-2836
PubMed: 22306467
DOI: 10.1016/J.JMB.2012.01.019
Page generated: Wed Dec 16 04:53:21 2020

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