Zinc in PDB 5vbn: Crystal Structure of Human Dna Polymerase Epsilon B-Subunit in Complex with C-Terminal Domain of Catalytic Subunit

Enzymatic activity of Crystal Structure of Human Dna Polymerase Epsilon B-Subunit in Complex with C-Terminal Domain of Catalytic Subunit

All present enzymatic activity of Crystal Structure of Human Dna Polymerase Epsilon B-Subunit in Complex with C-Terminal Domain of Catalytic Subunit:
2.7.7.7;

Protein crystallography data

The structure of Crystal Structure of Human Dna Polymerase Epsilon B-Subunit in Complex with C-Terminal Domain of Catalytic Subunit, PDB code: 5vbn was solved by A.G.Baranovskiy, J.Gu, Y.Suwa, N.D.Babayeva, T.H.Tahirov, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 39.75 / 2.35
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 92.260, 201.459, 78.336, 90.00, 90.00, 90.00
R / Rfree (%) 22.5 / 26.4

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Human Dna Polymerase Epsilon B-Subunit in Complex with C-Terminal Domain of Catalytic Subunit (pdb code 5vbn). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Crystal Structure of Human Dna Polymerase Epsilon B-Subunit in Complex with C-Terminal Domain of Catalytic Subunit, PDB code: 5vbn:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 5vbn

Go back to Zinc Binding Sites List in 5vbn
Zinc binding site 1 out of 4 in the Crystal Structure of Human Dna Polymerase Epsilon B-Subunit in Complex with C-Terminal Domain of Catalytic Subunit


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 Human Dna Polymerase Epsilon B-Subunit in Complex with C-Terminal Domain of Catalytic Subunit within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn2301

b:56.0
occ:1.00
 SG B:CYS2190 2.3 56.7 1.0
SG B:CYS2161 2.3 58.9 1.0
SG B:CYS2187 2.3 53.5 1.0
SG B:CYS2158 2.3 60.9 1.0
CB B:CYS2187 2.9 53.8 1.0
CB B:CYS2158 3.2 63.4 1.0
CB B:CYS2190 3.2 55.8 1.0
N B:CYS2190 3.6 56.0 1.0
CB B:CYS2161 3.6 63.3 1.0
CA B:CYS2190 3.9 56.2 1.0
O B:CYS2190 4.0 57.8 1.0
N B:CYS2161 4.1 64.2 1.0
C B:CYS2190 4.1 56.5 1.0
CA B:CYS2187 4.4 54.1 1.0
CA B:CYS2161 4.5 63.5 1.0
CB B:ALA2192 4.6 57.5 1.0
CB B:PHE2163 4.6 65.6 1.0
CA B:CYS2158 4.6 63.5 1.0
CB B:ASN2189 4.6 55.4 1.0
CB B:SER2160 4.7 65.3 1.0
ND2 B:ASN2189 4.8 55.6 1.0
C B:ASN2189 4.8 55.2 1.0
N B:ALA2192 4.8 56.2 1.0
C B:SER2160 4.9 64.6 1.0
C B:CYS2187 5.0 55.0 1.0

Zinc binding site 2 out of 4 in 5vbn

Go back to Zinc Binding Sites List in 5vbn
Zinc binding site 2 out of 4 in the Crystal Structure of Human Dna Polymerase Epsilon B-Subunit in Complex with C-Terminal Domain of Catalytic Subunit


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 Human Dna Polymerase Epsilon B-Subunit in Complex with C-Terminal Domain of Catalytic Subunit within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn2302

b:66.5
occ:1.00
 SG B:CYS2221 2.3 67.4 1.0
SG B:CYS2238 2.3 69.1 1.0
SG B:CYS2224 2.3 60.1 1.0
SG B:CYS2236 2.3 63.9 1.0
CB B:CYS2221 2.9 64.6 1.0
CB B:CYS2236 3.3 63.7 1.0
CB B:CYS2224 3.5 63.4 1.0
N B:CYS2224 3.6 63.8 1.0
CB B:CYS2238 3.9 69.2 1.0
O B:CYS2224 4.0 67.3 1.0
CA B:CYS2224 4.0 64.4 1.0
N B:CYS2238 4.4 68.2 1.0
CA B:CYS2221 4.4 63.6 1.0
C B:CYS2224 4.4 65.9 1.0
CB B:LYS2223 4.4 62.3 1.0
C B:LYS2223 4.7 62.9 1.0
CA B:CYS2236 4.7 64.5 1.0
N B:SER2237 4.7 67.2 1.0
CA B:CYS2238 4.8 68.4 1.0
N B:LYS2223 4.9 61.8 1.0
C B:CYS2221 4.9 62.6 1.0
CA B:LYS2223 5.0 62.0 1.0

Zinc binding site 3 out of 4 in 5vbn

Go back to Zinc Binding Sites List in 5vbn
Zinc binding site 3 out of 4 in the Crystal Structure of Human Dna Polymerase Epsilon B-Subunit in Complex with C-Terminal Domain of Catalytic Subunit


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 Human Dna Polymerase Epsilon B-Subunit in Complex with C-Terminal Domain of Catalytic Subunit within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn2301

b:62.5
occ:1.00
 SG F:CYS2161 2.3 61.7 1.0
SG F:CYS2190 2.3 60.0 1.0
SG F:CYS2187 2.3 56.9 1.0
SG F:CYS2158 2.3 69.8 1.0
CB F:CYS2187 3.2 59.6 1.0
CB F:CYS2190 3.2 60.8 1.0
CB F:CYS2158 3.2 71.5 1.0
CB F:CYS2161 3.4 66.3 1.0
N F:CYS2190 3.6 59.8 1.0
CA F:CYS2190 3.9 59.9 1.0
N F:CYS2161 3.9 67.7 1.0
O F:CYS2190 4.1 61.5 1.0
CA F:CYS2161 4.2 66.5 1.0
C F:CYS2190 4.2 60.1 1.0
CB F:PHE2163 4.5 68.2 1.0
CB F:SER2160 4.6 71.0 1.0
CB F:ASN2189 4.6 59.6 1.0
CA F:CYS2187 4.7 60.9 1.0
CA F:CYS2158 4.7 71.6 1.0
CB F:ALA2192 4.7 58.1 1.0
C F:SER2160 4.8 69.0 1.0
C F:ASN2189 4.8 59.7 1.0
ND2 F:ASN2189 4.8 61.9 1.0
C F:CYS2161 4.9 66.6 1.0
N F:PHE2163 4.9 67.9 1.0
N F:ASN2162 5.0 67.0 1.0

Zinc binding site 4 out of 4 in 5vbn

Go back to Zinc Binding Sites List in 5vbn
Zinc binding site 4 out of 4 in the Crystal Structure of Human Dna Polymerase Epsilon B-Subunit in Complex with C-Terminal Domain of Catalytic Subunit


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 Human Dna Polymerase Epsilon B-Subunit in Complex with C-Terminal Domain of Catalytic Subunit within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn2302

b:67.0
occ:1.00
 SG F:CYS2238 2.3 71.9 1.0
SG F:CYS2224 2.3 68.8 1.0
SG F:CYS2236 2.3 66.8 1.0
SG F:CYS2221 2.3 64.1 1.0
CB F:CYS2236 3.0 65.0 1.0
CB F:CYS2221 3.2 61.8 1.0
CB F:CYS2238 3.7 71.0 1.0
CB F:CYS2224 3.8 68.7 1.0
N F:CYS2238 3.9 70.5 1.0
N F:CYS2224 4.0 68.7 1.0
N F:SER2237 4.3 67.7 1.0
CA F:CYS2236 4.4 64.9 1.0
CA F:CYS2238 4.5 70.7 1.0
CA F:CYS2224 4.5 68.9 1.0
O F:CYS2224 4.5 71.0 1.0
CB F:LYS2223 4.6 67.6 1.0
CA F:CYS2221 4.7 61.6 1.0
C F:CYS2236 4.7 66.0 1.0
C F:CYS2224 4.8 69.4 1.0
C F:SER2237 5.0 69.8 1.0

Reference:

A.G.Baranovskiy, J.Gu, N.D.Babayeva, I.Kurinov, Y.I.Pavlov, T.H.Tahirov. Crystal Structure of the Human Pol B-Subunit in Complex with the C-Terminal Domain of the Catalytic Subunit. J. Biol. Chem. V. 292 15717 2017.
ISSN: ESSN 1083-351X
PubMed: 28747437
DOI: 10.1074/JBC.M117.792705
Page generated: Wed Dec 16 11:08:32 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy