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Nickel in PDB 1znv: How A His-Metal Finger Endonuclease COLE7 Binds and Cleaves Dna with A Transition Metal Ion Cofactor

Protein crystallography data

The structure of How A His-Metal Finger Endonuclease COLE7 Binds and Cleaves Dna with A Transition Metal Ion Cofactor, PDB code: 1znv was solved by L.G.Doudeva, H.Huang, K.C.Hsia, Z.Shi, C.L.Li, Y.Shen, H.S.Yuan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 27.65 / 2.00
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 119.021, 62.882, 74.769, 90.00, 90.00, 90.00
R / Rfree (%) 18.8 / 23.5

Nickel Binding Sites:

The binding sites of Nickel atom in the How A His-Metal Finger Endonuclease COLE7 Binds and Cleaves Dna with A Transition Metal Ion Cofactor (pdb code 1znv). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 2 binding sites of Nickel where determined in the How A His-Metal Finger Endonuclease COLE7 Binds and Cleaves Dna with A Transition Metal Ion Cofactor, PDB code: 1znv:
Jump to Nickel binding site number: 1; 2;

Nickel binding site 1 out of 2 in 1znv

Go back to Nickel Binding Sites List in 1znv
Nickel binding site 1 out of 2 in the How A His-Metal Finger Endonuclease COLE7 Binds and Cleaves Dna with A Transition Metal Ion Cofactor


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of How A His-Metal Finger Endonuclease COLE7 Binds and Cleaves Dna with A Transition Metal Ion Cofactor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ni580

b:33.7
occ:1.00
O3 B:PO4581 2.0 40.5 1.0
ND1 B:HIS544 2.0 32.5 1.0
NE2 B:HIS573 2.0 40.2 1.0
NE2 B:HIS569 2.1 28.7 1.0
CE1 B:HIS544 2.8 37.5 1.0
CE1 B:HIS573 2.9 45.1 1.0
P B:PO4581 3.0 57.0 1.0
CD2 B:HIS573 3.1 39.3 1.0
O2 B:PO4581 3.1 55.7 1.0
CD2 B:HIS569 3.1 34.7 1.0
CE1 B:HIS569 3.1 29.6 1.0
CG B:HIS544 3.1 41.4 1.0
O4 B:PO4581 3.6 62.4 1.0
CB B:HIS544 3.7 31.1 1.0
CA B:HIS544 3.8 31.0 1.0
NE2 B:HIS544 4.0 35.7 1.0
N B:GLU545 4.0 32.8 1.0
ND1 B:HIS573 4.0 40.9 1.0
CG B:HIS573 4.1 44.5 1.0
CD2 B:HIS544 4.2 38.2 1.0
O1 B:PO4581 4.2 51.7 1.0
ND1 B:HIS569 4.2 30.6 1.0
CG B:HIS569 4.3 29.2 1.0
O B:GLU545 4.4 34.6 1.0
C B:HIS544 4.4 28.1 1.0

Nickel binding site 2 out of 2 in 1znv

Go back to Nickel Binding Sites List in 1znv
Nickel binding site 2 out of 2 in the How A His-Metal Finger Endonuclease COLE7 Binds and Cleaves Dna with A Transition Metal Ion Cofactor


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of How A His-Metal Finger Endonuclease COLE7 Binds and Cleaves Dna with A Transition Metal Ion Cofactor within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ni580

b:38.1
occ:1.00
ND1 D:HIS544 2.0 39.3 1.0
NE2 D:HIS573 2.1 61.8 1.0
O2 D:PO4581 2.1 61.2 1.0
NE2 D:HIS569 2.1 38.4 1.0
O D:HOH1022 2.5 62.6 1.0
CE1 D:HIS573 2.7 58.0 1.0
O4 D:PO4581 2.7 66.8 1.0
CE1 D:HIS544 2.8 42.6 1.0
P D:PO4581 2.9 69.4 1.0
CD2 D:HIS569 3.1 32.0 1.0
CG D:HIS544 3.1 42.7 1.0
CE1 D:HIS569 3.2 34.4 1.0
CD2 D:HIS573 3.3 61.5 1.0
CB D:HIS544 3.6 35.7 1.0
O1 D:PO4581 3.7 75.4 1.0
CA D:HIS544 3.9 38.2 1.0
ND1 D:HIS573 3.9 58.2 1.0
NE2 D:HIS544 4.0 45.5 1.0
N D:GLU545 4.1 43.5 1.0
CD2 D:HIS544 4.2 39.3 1.0
O3 D:PO4581 4.2 64.1 1.0
CG D:HIS569 4.2 33.8 1.0
CG D:HIS573 4.2 59.7 1.0
ND1 D:HIS569 4.3 30.5 1.0
O D:GLU545 4.4 42.4 1.0
C D:HIS544 4.5 39.2 1.0
O D:HOH983 4.7 45.7 1.0

Reference:

L.G.Doudeva, H.Huang, K.C.Hsia, Z.Shi, C.L.Li, Y.Shen, Y.S.Cheng, H.S.Yuan. Crystal Structural Analysis and Metal-Dependent Stability and Activity Studies of the COLE7 Endonuclease Domain in Complex with Dna/ZN2+ or Inhibitor/NI2+ Protein Sci. V. 15 269 2006.
ISSN: ISSN 0961-8368
PubMed: 16434744
DOI: 10.1110/PS.051903406
Page generated: Fri Sep 25 08:04:58 2020
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