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Zinc in PDB 4y97: Crystal Structure of Human Pol Alpha B-Subunit in Complex with C- Terminal Domain of Catalytic Subunit

Enzymatic activity of Crystal Structure of Human Pol Alpha B-Subunit in Complex with C- Terminal Domain of Catalytic Subunit

All present enzymatic activity of Crystal Structure of Human Pol Alpha 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 Pol Alpha B-Subunit in Complex with C- Terminal Domain of Catalytic Subunit, PDB code: 4y97 was solved by Y.Suwa, J.Gu, A.G.Baranovskiy, 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) 47.68 / 2.51
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 103.593, 137.135, 132.092, 90.00, 100.97, 90.00
R / Rfree (%) 21.8 / 25.7

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Human Pol Alpha B-Subunit in Complex with C- Terminal Domain of Catalytic Subunit (pdb code 4y97). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the Crystal Structure of Human Pol Alpha B-Subunit in Complex with C- Terminal Domain of Catalytic Subunit, PDB code: 4y97:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 4y97

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Zinc binding site 1 out of 8 in the Crystal Structure of Human Pol Alpha 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 Pol Alpha B-Subunit in Complex with C- Terminal Domain of Catalytic Subunit within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1501

b:82.8
occ:1.00
 SG B:CYS1286 2.3 72.2 1.0
SG B:CYS1310 2.3 56.9 1.0
SG B:CYS1315 2.3 0.1 1.0
SG B:CYS1283 2.3 87.5 1.0
CB B:CYS1315 2.9 0.1 1.0
CB B:CYS1283 3.0 79.7 1.0
CB B:CYS1310 3.0 68.4 1.0
CB B:CYS1286 3.5 70.9 1.0
N B:CYS1286 4.0 71.1 1.0
CG2 B:THR1288 4.1 66.9 1.0
CA B:CYS1286 4.3 72.4 1.0
CA B:CYS1315 4.3 98.2 1.0
CA B:CYS1310 4.4 76.1 1.0
CA B:CYS1283 4.5 79.0 1.0
CB B:ASN1312 4.5 90.2 1.0
CB B:ALA1317 4.7 83.3 1.0
C B:CYS1315 4.8 96.3 1.0
O B:ALA1317 4.8 88.3 1.0
N B:GLY1287 4.9 74.4 1.0
CB B:THR1285 4.9 77.0 1.0
O B:CYS1315 5.0 93.2 1.0
O B:ASN1312 5.0 90.9 1.0

Zinc binding site 2 out of 8 in 4y97

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Zinc binding site 2 out of 8 in the Crystal Structure of Human Pol Alpha 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 Pol Alpha B-Subunit in Complex with C- Terminal Domain of Catalytic Subunit within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1502

b:37.5
occ:1.00
 SG B:CYS1348 2.3 33.5 1.0
SG B:CYS1353 2.3 34.8 1.0
SG B:CYS1371 2.3 34.5 1.0
SG B:CYS1374 2.3 35.1 1.0
CB B:CYS1371 2.9 23.4 1.0
CB B:CYS1353 3.1 38.5 1.0
CB B:CYS1348 3.3 34.6 1.0
CB B:CYS1374 3.3 26.9 1.0
N B:CYS1374 3.5 36.9 1.0
O B:CYS1374 3.9 55.9 1.0
CA B:CYS1374 4.0 36.1 1.0
CB B:ALA1373 4.3 37.8 1.0
CB B:ALA1377 4.3 32.6 1.0
C B:CYS1374 4.3 43.5 1.0
CB B:ASN1355 4.3 33.4 1.0
CA B:CYS1371 4.4 30.9 1.0
CA B:CYS1353 4.6 40.0 1.0
CA B:CYS1348 4.6 30.6 1.0
C B:ALA1373 4.7 34.1 1.0
C B:CYS1371 4.8 27.6 1.0
N B:ALA1373 4.8 35.5 1.0
N B:ASN1355 4.9 31.4 1.0
CA B:ALA1373 4.9 31.3 1.0
CB B:GLU1350 4.9 35.0 1.0
N B:ARG1354 4.9 34.5 1.0

Zinc binding site 3 out of 8 in 4y97

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Zinc binding site 3 out of 8 in the Crystal Structure of Human Pol Alpha 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 Pol Alpha B-Subunit in Complex with C- Terminal Domain of Catalytic Subunit within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn1501

b:66.5
occ:1.00
 SG D:CYS1310 2.3 54.6 1.0
SG D:CYS1315 2.3 80.8 1.0
SG D:CYS1286 2.3 70.4 1.0
SG D:CYS1283 2.3 61.5 1.0
CB D:CYS1315 2.8 78.6 1.0
CB D:CYS1283 2.9 53.9 1.0
CB D:CYS1286 3.1 66.7 1.0
CB D:CYS1310 3.4 51.7 1.0
N D:CYS1286 3.7 62.7 1.0
CA D:CYS1286 3.9 64.0 1.0
OG1 D:THR1288 4.3 57.6 1.0
CA D:CYS1315 4.3 76.9 1.0
CB D:ASN1312 4.4 79.9 1.0
CA D:CYS1283 4.5 52.9 1.0
N D:GLY1287 4.6 61.9 1.0
ND2 D:ASN1312 4.6 76.4 1.0
C D:CYS1286 4.6 64.0 1.0
CA D:CYS1310 4.7 55.9 1.0
C D:THR1285 4.9 60.9 1.0
C D:CYS1315 4.9 74.8 1.0
CB D:THR1285 5.0 58.8 1.0

Zinc binding site 4 out of 8 in 4y97

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Zinc binding site 4 out of 8 in the Crystal Structure of Human Pol Alpha 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 Pol Alpha B-Subunit in Complex with C- Terminal Domain of Catalytic Subunit within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn1502

b:43.8
occ:1.00
 SG D:CYS1353 2.3 58.5 1.0
SG D:CYS1374 2.3 53.9 1.0
SG D:CYS1348 2.3 37.9 1.0
SG D:CYS1371 2.3 46.1 1.0
CB D:CYS1353 3.0 56.3 1.0
CB D:CYS1371 3.1 31.4 1.0
CB D:CYS1348 3.1 41.2 1.0
CB D:CYS1374 3.5 56.1 1.0
N D:CYS1374 3.8 57.9 1.0
O D:CYS1374 4.0 68.0 1.0
CB D:ALA1377 4.0 61.0 1.0
CA D:CYS1374 4.2 57.7 1.0
CA D:CYS1353 4.4 58.4 1.0
CB D:ASN1355 4.4 45.4 1.0
CB D:ALA1373 4.5 54.1 1.0
C D:CYS1374 4.5 60.3 1.0
CA D:CYS1348 4.5 42.0 1.0
CA D:CYS1371 4.5 35.1 1.0
CB D:GLU1350 4.7 61.9 1.0
N D:ARG1354 4.8 53.9 1.0
N D:ASN1355 4.8 43.2 1.0
C D:CYS1353 4.9 56.8 1.0
C D:ALA1373 4.9 57.7 1.0

Zinc binding site 5 out of 8 in 4y97

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Zinc binding site 5 out of 8 in the Crystal Structure of Human Pol Alpha 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 5 of Crystal Structure of Human Pol Alpha B-Subunit in Complex with C- Terminal Domain of Catalytic Subunit within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn1501

b:53.2
occ:1.00
 SG F:CYS1315 2.3 64.6 1.0
SG F:CYS1286 2.3 66.0 1.0
SG F:CYS1310 2.3 52.0 1.0
SG F:CYS1283 2.3 50.1 1.0
CB F:CYS1315 2.8 72.0 1.0
CB F:CYS1283 2.9 40.8 1.0
CB F:CYS1286 3.0 66.3 1.0
CB F:CYS1310 3.4 43.5 1.0
N F:CYS1286 3.6 61.0 1.0
CA F:CYS1286 3.8 63.5 1.0
CA F:CYS1315 4.4 76.9 1.0
CB F:ASN1312 4.4 86.2 1.0
CA F:CYS1283 4.4 46.9 1.0
N F:GLY1287 4.5 62.9 1.0
C F:CYS1286 4.6 64.5 1.0
CA F:CYS1310 4.8 43.4 1.0
CB F:THR1285 4.8 53.5 1.0
C F:THR1285 4.8 58.4 1.0
N F:THR1288 5.0 58.3 1.0
C F:CYS1315 5.0 71.9 1.0
CB F:ALA1317 5.0 60.0 1.0

Zinc binding site 6 out of 8 in 4y97

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Zinc binding site 6 out of 8 in the Crystal Structure of Human Pol Alpha 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 6 of Crystal Structure of Human Pol Alpha B-Subunit in Complex with C- Terminal Domain of Catalytic Subunit within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn1502

b:62.5
occ:1.00
 SG F:CYS1348 2.3 68.5 1.0
SG F:CYS1353 2.3 55.8 1.0
SG F:CYS1374 2.3 78.6 1.0
SG F:CYS1371 2.3 50.3 1.0
CB F:CYS1353 3.0 65.5 1.0
CB F:CYS1371 3.0 40.9 1.0
CB F:CYS1348 3.0 62.1 1.0
CB F:CYS1374 3.5 69.9 1.0
N F:CYS1374 3.8 69.0 1.0
O F:CYS1374 4.1 76.6 1.0
CB F:ALA1377 4.1 69.7 1.0
CA F:CYS1374 4.2 69.0 1.0
CB F:ASN1355 4.4 57.9 1.0
CB F:ALA1373 4.4 64.9 1.0
CA F:CYS1353 4.4 70.0 1.0
CA F:CYS1348 4.5 61.1 1.0
CA F:CYS1371 4.5 49.1 1.0
C F:CYS1374 4.5 70.2 1.0
N F:ASN1355 4.7 62.7 1.0
N F:ARG1354 4.8 74.3 1.0
CB F:GLU1350 4.8 77.9 1.0
C F:CYS1353 4.9 71.5 1.0
C F:ALA1373 4.9 67.7 1.0

Zinc binding site 7 out of 8 in 4y97

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Zinc binding site 7 out of 8 in the Crystal Structure of Human Pol Alpha 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 7 of Crystal Structure of Human Pol Alpha B-Subunit in Complex with C- Terminal Domain of Catalytic Subunit within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Zn1501

b:88.3
occ:1.00
 SG H:CYS1283 2.3 94.7 1.0
SG H:CYS1315 2.3 99.2 1.0
SG H:CYS1286 2.3 89.6 1.0
SG H:CYS1310 2.3 73.4 1.0
CB H:CYS1283 2.8 92.2 1.0
CB H:CYS1315 3.0 0.9 1.0
CB H:CYS1286 3.1 86.5 1.0
CB H:CYS1310 3.5 75.3 1.0
N H:CYS1286 3.6 89.6 1.0
OG1 H:THR1285 3.7 97.3 1.0
CA H:CYS1286 3.9 88.8 1.0
CA H:CYS1283 4.3 89.8 1.0
OG1 H:THR1288 4.5 86.3 1.0
CA H:CYS1315 4.5 0.6 1.0
N H:GLY1287 4.5 89.4 1.0
CB H:ASN1312 4.6 99.8 1.0
C H:CYS1286 4.6 89.2 1.0
C H:THR1285 4.8 90.8 1.0
CA H:CYS1310 4.8 82.0 1.0
CB H:THR1285 4.8 90.6 1.0
CB H:ALA1317 4.9 79.2 1.0
C H:CYS1283 4.9 90.8 1.0
N H:THR1288 5.0 86.5 1.0

Zinc binding site 8 out of 8 in 4y97

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Zinc binding site 8 out of 8 in the Crystal Structure of Human Pol Alpha 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 8 of Crystal Structure of Human Pol Alpha B-Subunit in Complex with C- Terminal Domain of Catalytic Subunit within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Zn1502

b:64.2
occ:1.00
 SG H:CYS1348 2.3 59.8 1.0
SG H:CYS1353 2.3 68.4 1.0
SG H:CYS1374 2.3 74.8 1.0
SG H:CYS1371 2.3 66.0 1.0
CB H:CYS1353 2.9 74.2 1.0
CB H:CYS1348 3.0 59.3 1.0
CB H:CYS1371 3.1 54.0 1.0
CB H:CYS1374 3.5 74.0 1.0
N H:CYS1374 3.9 73.7 1.0
CB H:ALA1377 4.0 63.8 1.0
O H:CYS1374 4.2 77.6 1.0
CA H:CYS1374 4.2 71.5 1.0
CA H:CYS1353 4.3 78.5 1.0
CA H:CYS1348 4.4 61.1 1.0
CB H:ASN1355 4.4 71.2 1.0
CB H:ALA1373 4.6 72.8 1.0
C H:CYS1374 4.6 69.6 1.0
CA H:CYS1371 4.6 55.4 1.0
CB H:GLU1350 4.6 77.0 1.0
N H:ARG1354 4.7 78.8 1.0
N H:ASN1355 4.7 72.8 1.0
C H:CYS1353 4.8 79.2 1.0

Reference:

Y.Suwa, J.Gu, A.G.Baranovskiy, N.D.Babayeva, Y.I.Pavlov, T.H.Tahirov. Crystal Structure of the Human Pol Alpha B Subunit in Complex with the C-Terminal Domain of the Catalytic Subunit. J.Biol.Chem. 2015.
ISSN: ESSN 1083-351X
PubMed: 25847248
DOI: 10.1074/JBC.M115.649954
Page generated: Sun Oct 27 11:02:12 2024

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