Atomistry » Zinc » PDB 4y8a-4ylo » 4y97
Atomistry »
  Zinc »
    PDB 4y8a-4ylo »
      4y97 »

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

Go back to Zinc Binding Sites List in 4y97
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

Go back to Zinc Binding Sites List in 4y97
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

Go back to Zinc Binding Sites List in 4y97
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

Go back to Zinc Binding Sites List in 4y97
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

Go back to Zinc Binding Sites List in 4y97
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

Go back to Zinc Binding Sites List in 4y97
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

Go back to Zinc Binding Sites List in 4y97
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

Go back to Zinc Binding Sites List in 4y97
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

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy