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Zinc in PDB 2jbg: Crystal Structure of the Mutant N560A of the Nuclease Domain of COLE7 in Complex with IM7

Protein crystallography data

The structure of Crystal Structure of the Mutant N560A of the Nuclease Domain of COLE7 in Complex with IM7, PDB code: 2jbg was solved by H.Huang, H.S.Yuan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 37.40 / 2.20
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 119.180, 62.683, 74.785, 90.00, 90.00, 90.00
R / Rfree (%) 20.2 / 24.9

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of the Mutant N560A of the Nuclease Domain of COLE7 in Complex with IM7 (pdb code 2jbg). 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 N560A of the Nuclease Domain of COLE7 in Complex with IM7, PDB code: 2jbg:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 2jbg

Go back to Zinc Binding Sites List in 2jbg
Zinc binding site 1 out of 2 in the Crystal Structure of the Mutant N560A of the Nuclease Domain of COLE7 in Complex with IM7


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 N560A of the Nuclease Domain of COLE7 in Complex with IM7 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1577

b:36.1
occ:1.00
ND1 B:HIS544 1.9 34.2 1.0
O1 B:SO41578 2.0 47.5 1.0
NE2 B:HIS573 2.0 45.2 1.0
NE2 B:HIS569 2.2 28.4 1.0
CE1 B:HIS544 2.8 35.0 1.0
S B:SO41578 2.9 50.1 1.0
CE1 B:HIS573 2.9 43.8 1.0
O4 B:SO41578 3.0 49.4 1.0
CD2 B:HIS569 3.0 28.0 1.0
CD2 B:HIS573 3.0 44.4 1.0
CG B:HIS544 3.1 36.7 1.0
CE1 B:HIS569 3.2 26.0 1.0
O2 B:SO41578 3.5 51.8 1.0
CB B:HIS544 3.6 32.6 1.0
CA B:HIS544 3.7 31.1 1.0
NE2 B:HIS544 3.9 37.6 1.0
ND1 B:HIS573 4.0 45.0 1.0
N B:HIS545 4.0 34.2 1.0
CD2 B:HIS544 4.1 35.9 1.0
CG B:HIS573 4.1 45.4 1.0
O3 B:SO41578 4.2 49.2 1.0
CG B:HIS569 4.2 29.4 1.0
ND1 B:HIS569 4.3 29.4 1.0
C B:HIS544 4.4 31.7 1.0
O B:HIS545 4.5 39.0 1.0
O B:LEU543 4.8 26.8 1.0
O B:HOH2077 4.9 51.6 1.0
N B:HIS544 4.9 29.2 1.0

Zinc binding site 2 out of 2 in 2jbg

Go back to Zinc Binding Sites List in 2jbg
Zinc binding site 2 out of 2 in the Crystal Structure of the Mutant N560A of the Nuclease Domain of COLE7 in Complex with IM7


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 N560A of the Nuclease Domain of COLE7 in Complex with IM7 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn1577

b:39.5
occ:1.00
O4 D:SO41578 1.9 45.9 1.0
ND1 D:HIS544 2.1 42.7 1.0
NE2 D:HIS573 2.1 42.2 1.0
NE2 D:HIS569 2.1 29.2 1.0
S D:SO41578 2.8 51.5 1.0
O3 D:SO41578 2.9 49.3 1.0
CE1 D:HIS573 2.9 41.3 1.0
CD2 D:HIS569 2.9 29.1 1.0
CE1 D:HIS544 3.0 43.2 1.0
CG D:HIS544 3.1 42.2 1.0
CD2 D:HIS573 3.2 41.3 1.0
CE1 D:HIS569 3.3 27.1 1.0
O2 D:SO41578 3.3 52.5 1.0
CB D:HIS544 3.5 38.7 1.0
CA D:HIS544 3.7 37.5 1.0
N D:HIS545 4.0 42.6 1.0
ND1 D:HIS573 4.1 41.2 1.0
O1 D:SO41578 4.1 48.2 1.0
NE2 D:HIS544 4.1 44.5 1.0
CG D:HIS569 4.1 27.6 1.0
CD2 D:HIS544 4.2 42.5 1.0
CG D:HIS573 4.3 41.8 1.0
ND1 D:HIS569 4.3 26.4 1.0
C D:HIS544 4.4 39.5 1.0
O D:HIS545 4.5 48.1 1.0
O D:LEU543 4.7 33.7 1.0
N D:HIS544 4.8 35.4 1.0

Reference:

H.Huang, H.S.Yuan. The Conserved Asparagine in the Hnh Motif Serves An Important Structural Role in Metal Finger Endonucleases. J.Mol.Biol. V. 368 812 2007.
ISSN: ISSN 0022-2836
PubMed: 17368670
DOI: 10.1016/J.JMB.2007.02.044
Page generated: Wed Dec 16 03:31:58 2020

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