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Zinc in PDB 1mz8: Crystal Structures of the Nuclease Domain of COLE7/IM7 in Complex with A Phosphate Ion and A Zinc Ion

Protein crystallography data

The structure of Crystal Structures of the Nuclease Domain of COLE7/IM7 in Complex with A Phosphate Ion and A Zinc Ion, PDB code: 1mz8 was solved by M.J.Sui, L.C.Tsai, K.C.Hsia, L.G.Doudeva, W.Y.Ku, G.W.Han, H.S.Yuan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 27.97 / 2.00
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 119.735, 62.410, 74.137, 90.00, 90.00, 90.00
R / Rfree (%) 18.3 / 23

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structures of the Nuclease Domain of COLE7/IM7 in Complex with A Phosphate Ion and A Zinc Ion (pdb code 1mz8). 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 Structures of the Nuclease Domain of COLE7/IM7 in Complex with A Phosphate Ion and A Zinc Ion, PDB code: 1mz8:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 1mz8

Go back to Zinc Binding Sites List in 1mz8
Zinc binding site 1 out of 2 in the Crystal Structures of the Nuclease Domain of COLE7/IM7 in Complex with A Phosphate Ion and A Zinc Ion


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structures of the Nuclease Domain of COLE7/IM7 in Complex with A Phosphate Ion and A Zinc Ion within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn600

b:39.1
occ:1.00
ND1 B:HIS544 2.0 30.3 1.0
O3 B:PO4601 2.0 33.0 1.0
NE2 B:HIS573 2.1 34.2 1.0
NE2 B:HIS569 2.2 24.6 1.0
CE1 B:HIS544 2.9 29.7 1.0
CE1 B:HIS573 3.0 35.0 1.0
CD2 B:HIS569 3.0 25.6 1.0
CG B:HIS544 3.1 30.0 1.0
CD2 B:HIS573 3.1 35.4 1.0
P B:PO4601 3.2 35.6 1.0
CE1 B:HIS569 3.3 24.8 1.0
O2 B:PO4601 3.4 37.3 1.0
CB B:HIS544 3.5 27.2 1.0
CA B:HIS544 3.6 26.3 1.0
O4 B:PO4601 3.9 38.6 1.0
N B:HIS545 4.0 28.0 1.0
NE2 B:HIS544 4.0 29.9 1.0
ND1 B:HIS573 4.1 37.0 1.0
CD2 B:HIS544 4.1 30.1 1.0
CG B:HIS573 4.2 38.0 1.0
CG B:HIS569 4.2 25.5 1.0
C B:HIS544 4.3 26.4 1.0
ND1 B:HIS569 4.4 26.1 1.0
O1 B:PO4601 4.4 34.5 1.0
O B:HIS545 4.6 32.2 1.0
O B:LEU543 4.6 23.6 1.0
N B:HIS544 4.8 24.0 1.0

Zinc binding site 2 out of 2 in 1mz8

Go back to Zinc Binding Sites List in 1mz8
Zinc binding site 2 out of 2 in the Crystal Structures of the Nuclease Domain of COLE7/IM7 in Complex with A Phosphate Ion and A Zinc Ion


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structures of the Nuclease Domain of COLE7/IM7 in Complex with A Phosphate Ion and A Zinc Ion within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn600

b:37.0
occ:1.00
O4 D:PO4601 2.1 34.0 1.0
ND1 D:HIS544 2.1 30.7 1.0
NE2 D:HIS569 2.1 22.6 1.0
NE2 D:HIS573 2.2 34.6 1.0
CE1 D:HIS544 3.0 31.5 1.0
CD2 D:HIS569 3.0 24.6 1.0
CE1 D:HIS573 3.1 34.4 1.0
CE1 D:HIS569 3.1 24.8 1.0
P D:PO4601 3.1 37.9 1.0
CG D:HIS544 3.2 30.5 1.0
CD2 D:HIS573 3.2 35.1 1.0
O1 D:PO4601 3.2 37.9 1.0
CB D:HIS544 3.5 26.8 1.0
CA D:HIS544 3.7 27.4 1.0
O3 D:PO4601 3.9 40.0 1.0
N D:HIS545 4.0 27.9 1.0
NE2 D:HIS544 4.1 31.6 1.0
CG D:HIS569 4.1 25.4 1.0
O D:HOH1033 4.2 35.4 1.0
ND1 D:HIS569 4.2 24.5 1.0
ND1 D:HIS573 4.2 35.8 1.0
CD2 D:HIS544 4.2 29.9 1.0
CG D:HIS573 4.3 35.1 1.0
O2 D:PO4601 4.3 35.3 1.0
C D:HIS544 4.3 27.0 1.0
O D:HIS545 4.5 30.1 1.0
O D:HOH1005 4.5 43.1 1.0
O D:LEU543 4.7 25.9 1.0
N D:HIS544 4.9 26.1 1.0

Reference:

M.J.Sui, L.C.Tsai, K.C.Hsia, L.G.Doudeva, W.Y.Ku, G.W.Han, H.S.Yuan. Metal Ions and Phosphate Binding in the H-N-H Motif: Crystal Structures of the Nuclease Domain of COLE7/IM7 in Complex with A Phosphate Ion and Different Divalent Metal Ions Protein Sci. V. 11 2947 2002.
ISSN: ISSN 0961-8368
PubMed: 12441392
DOI: 10.1110/PS.0220602
Page generated: Fri Sep 25 22:40:06 2020
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