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Zinc in PDB 2zvl: Crystal Structure of Pcna in Complex with Dna Polymerase Kappa Fragment

Enzymatic activity of Crystal Structure of Pcna in Complex with Dna Polymerase Kappa Fragment

All present enzymatic activity of Crystal Structure of Pcna in Complex with Dna Polymerase Kappa Fragment:
2.7.7.7;

Protein crystallography data

The structure of Crystal Structure of Pcna in Complex with Dna Polymerase Kappa Fragment, PDB code: 2zvl was solved by A.Hishiki, H.Hashimoto, T.Hanafusa, K.Kamei, E.Ohashi, T.Shimizu, H.Ohmori, M.Sato, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 2.50
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 74.769, 74.707, 109.049, 87.25, 77.46, 80.26
R / Rfree (%) 22.5 / 28.9

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Pcna in Complex with Dna Polymerase Kappa Fragment (pdb code 2zvl). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the Crystal Structure of Pcna in Complex with Dna Polymerase Kappa Fragment, PDB code: 2zvl:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 2zvl

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Zinc binding site 1 out of 6 in the Crystal Structure of Pcna in Complex with Dna Polymerase Kappa Fragment


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 Pcna in Complex with Dna Polymerase Kappa Fragment within 5.0Å range:
probe atom residue distance (Å) B Occ
V:Zn1

b:47.2
occ:1.00
 OD2 V:ASP866 2.1 33.9 1.0
ND1 V:HIS863 2.1 21.6 1.0
ND1 B:HIS44 2.1 26.9 1.0
OD1 V:ASP866 2.6 31.4 1.0
CG V:ASP866 2.7 33.5 1.0
CE1 V:HIS863 3.0 29.6 1.0
CG B:HIS44 3.1 27.0 1.0
CG V:HIS863 3.1 31.1 1.0
CE1 B:HIS44 3.1 26.1 1.0
CB B:HIS44 3.4 26.5 1.0
CB V:HIS863 3.5 36.8 1.0
CA V:HIS863 4.0 37.4 1.0
O V:HOH324 4.0 20.9 1.0
NE2 V:HIS863 4.2 27.8 1.0
CB V:ASP866 4.2 37.7 1.0
CD2 V:HIS863 4.2 30.6 1.0
CD2 B:HIS44 4.2 27.3 1.0
NE2 B:HIS44 4.2 27.6 1.0
N V:HIS863 4.8 39.2 1.0
CE B:MET40 4.9 36.4 1.0
CA B:HIS44 4.9 28.0 1.0

Zinc binding site 2 out of 6 in 2zvl

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Zinc binding site 2 out of 6 in the Crystal Structure of Pcna in Complex with Dna Polymerase Kappa Fragment


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 Pcna in Complex with Dna Polymerase Kappa Fragment within 5.0Å range:
probe atom residue distance (Å) B Occ
W:Zn2

b:45.7
occ:1.00
 OD2 W:ASP866 1.9 9.8 1.0
ND1 C:HIS44 1.9 39.1 1.0
ND1 W:HIS863 2.1 32.1 1.0
CE1 C:HIS44 2.8 30.0 1.0
CG W:ASP866 2.8 28.8 1.0
CG C:HIS44 2.9 32.9 1.0
CE1 W:HIS863 2.9 34.7 1.0
OD1 W:ASP866 3.1 31.6 1.0
CG W:HIS863 3.2 29.3 1.0
CB C:HIS44 3.3 32.7 1.0
CB W:HIS863 3.6 29.7 1.0
NE2 C:HIS44 3.9 40.8 1.0
CD2 C:HIS44 4.0 36.2 1.0
CA W:HIS863 4.0 31.4 1.0
NE2 W:HIS863 4.1 29.5 1.0
CD2 W:HIS863 4.2 27.7 1.0
CB W:ASP866 4.3 29.6 1.0
N W:HIS863 4.7 34.3 1.0
CA C:HIS44 4.8 32.3 1.0

Zinc binding site 3 out of 6 in 2zvl

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Zinc binding site 3 out of 6 in the Crystal Structure of Pcna in Complex with Dna Polymerase Kappa Fragment


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of Pcna in Complex with Dna Polymerase Kappa Fragment within 5.0Å range:
probe atom residue distance (Å) B Occ
Y:Zn3

b:48.8
occ:1.00
 OD2 Y:ASP866 1.8 40.6 1.0
ND1 Y:HIS863 1.8 12.6 1.0
ND1 E:HIS44 2.0 27.8 1.0
CE1 Y:HIS863 2.5 24.5 1.0
CG Y:ASP866 2.8 35.9 1.0
CG E:HIS44 3.0 30.2 1.0
CE1 E:HIS44 3.0 29.8 1.0
CG Y:HIS863 3.0 27.6 1.0
OD1 Y:ASP866 3.2 31.3 1.0
CB E:HIS44 3.3 28.0 1.0
NE2 Y:HIS863 3.7 25.5 1.0
CB Y:HIS863 3.7 32.7 1.0
CA Y:HIS863 3.9 33.6 1.0
CD2 Y:HIS863 4.0 27.2 1.0
NE2 E:HIS44 4.1 28.6 1.0
CD2 E:HIS44 4.1 31.3 1.0
CB Y:ASP866 4.1 36.4 1.0
N Y:HIS863 4.8 33.1 1.0
CA E:HIS44 4.9 31.2 1.0
C Y:HIS863 4.9 31.8 1.0

Zinc binding site 4 out of 6 in 2zvl

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Zinc binding site 4 out of 6 in the Crystal Structure of Pcna in Complex with Dna Polymerase Kappa Fragment


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of Pcna in Complex with Dna Polymerase Kappa Fragment within 5.0Å range:
probe atom residue distance (Å) B Occ
Z:Zn4

b:47.2
occ:1.00
 OD2 Z:ASP866 2.0 2.0 1.0
ND1 Z:HIS863 2.1 30.4 1.0
ND1 F:HIS44 2.3 32.2 1.0
CE1 Z:HIS863 2.6 29.8 1.0
CE1 F:HIS44 2.9 22.5 1.0
CG Z:ASP866 3.0 22.4 1.0
CG F:HIS44 3.1 29.0 1.0
CG Z:HIS863 3.3 26.0 1.0
OD1 Z:ASP866 3.4 32.8 1.0
CB F:HIS44 3.6 23.8 1.0
NE2 Z:HIS863 3.8 28.4 1.0
NE2 F:HIS44 3.9 33.2 1.0
CB Z:HIS863 4.0 25.8 1.0
CD2 F:HIS44 4.0 32.1 1.0
CD2 Z:HIS863 4.2 19.9 1.0
CB Z:ASP866 4.5 20.2 1.0
CA Z:HIS863 4.7 27.2 1.0
O Z:HIS863 4.9 29.5 1.0
CA F:HIS44 5.0 28.4 1.0

Zinc binding site 5 out of 6 in 2zvl

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Zinc binding site 5 out of 6 in the Crystal Structure of Pcna in Complex with Dna Polymerase Kappa Fragment


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Crystal Structure of Pcna in Complex with Dna Polymerase Kappa Fragment within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn262

b:54.4
occ:1.00
 ND1 E:HIS246 2.1 36.2 1.0
O E:HOH374 2.1 15.8 1.0
CE1 E:HIS246 3.0 36.0 1.0
CG E:HIS246 3.2 25.3 1.0
CB E:HIS246 3.7 26.8 1.0
C E:GLY245 4.0 24.0 1.0
N E:HIS246 4.0 26.1 1.0
NE2 E:HIS246 4.1 32.5 1.0
CA E:GLY245 4.2 25.0 1.0
NH2 E:ARG53 4.2 31.1 1.0
CD2 E:HIS246 4.3 28.7 1.0
O E:GLY245 4.4 23.9 1.0
CA E:HIS246 4.5 27.1 1.0
NE E:ARG53 4.8 32.7 1.0
OE2 E:GLU238 4.9 46.2 1.0
CZ E:ARG53 5.0 31.8 1.0

Zinc binding site 6 out of 6 in 2zvl

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Zinc binding site 6 out of 6 in the Crystal Structure of Pcna in Complex with Dna Polymerase Kappa Fragment


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Crystal Structure of Pcna in Complex with Dna Polymerase Kappa Fragment within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn262

b:51.7
occ:1.00
 ND1 B:HIS246 2.1 35.6 1.0
O B:HOH375 2.2 10.5 1.0
CE1 B:HIS246 2.9 43.3 1.0
CG B:HIS246 3.2 34.5 1.0
CB B:HIS246 3.6 31.0 1.0
N B:HIS246 4.0 31.3 1.0
C B:GLY245 4.0 31.0 1.0
NE2 B:HIS246 4.1 39.1 1.0
CD2 B:HIS246 4.2 40.8 1.0
CA B:GLY245 4.3 31.5 1.0
NH1 B:ARG53 4.4 28.4 1.0
O B:GLY245 4.4 31.3 1.0
CA B:HIS246 4.4 30.8 1.0
NZ B:LYS248 4.9 34.0 1.0

Reference:

A.Hishiki, H.Hashimoto, T.Hanafusa, K.Kamei, E.Ohashi, T.Shimizu, H.Ohmori, M.Sato. Structural Basis For Novel Interactions Between Human Translesion Synthesis Polymerases and Proliferating Cell Nuclear Antigen J.Biol.Chem. V. 284 10552 2009.
ISSN: ISSN 0021-9258
PubMed: 19208623
DOI: 10.1074/JBC.M809745200
Page generated: Wed Dec 16 04:05:48 2020

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