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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

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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

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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: Mon Oct 28 12:46:36 2024

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