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Zinc in PDB 3flo: Crystal Structure of the Carboxyl-Terminal Domain of Yeast Dna Polymerase Alpha in Complex with Its B Subunit

Enzymatic activity of Crystal Structure of the Carboxyl-Terminal Domain of Yeast Dna Polymerase Alpha in Complex with Its B Subunit

All present enzymatic activity of Crystal Structure of the Carboxyl-Terminal Domain of Yeast Dna Polymerase Alpha in Complex with Its B Subunit:
2.7.7.7;

Protein crystallography data

The structure of Crystal Structure of the Carboxyl-Terminal Domain of Yeast Dna Polymerase Alpha in Complex with Its B Subunit, PDB code: 3flo was solved by S.N.Klinge, L.Pellegrini, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 31.90 / 2.50
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 85.411, 142.633, 175.255, 90.00, 102.33, 90.00
R / Rfree (%) 19.1 / 21.8

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of the Carboxyl-Terminal Domain of Yeast Dna Polymerase Alpha in Complex with Its B Subunit (pdb code 3flo). 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 the Carboxyl-Terminal Domain of Yeast Dna Polymerase Alpha in Complex with Its B Subunit, PDB code: 3flo:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 3flo

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Zinc binding site 1 out of 8 in the Crystal Structure of the Carboxyl-Terminal Domain of Yeast Dna Polymerase Alpha in Complex with Its B 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 the Carboxyl-Terminal Domain of Yeast Dna Polymerase Alpha in Complex with Its B Subunit within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1

b:59.5
occ:1.00
 SG B:CYS1290 2.3 47.2 1.0
SG B:CYS1314 2.3 45.3 1.0
SG B:CYS1287 2.4 43.7 1.0
SG B:CYS1317 2.4 55.1 1.0
CB B:CYS1317 3.3 58.2 1.0
CB B:CYS1314 3.3 44.1 1.0
CB B:CYS1290 3.3 54.1 1.0
CB B:CYS1287 3.3 40.6 1.0
N B:CYS1317 3.8 56.9 1.0
N B:CYS1290 3.9 51.0 1.0
CA B:CYS1317 4.1 58.9 1.0
CA B:CYS1290 4.2 52.9 1.0
CB B:HIS1316 4.6 56.1 1.0
CB B:SER1289 4.7 53.3 1.0
CA B:CYS1314 4.7 44.2 1.0
C B:HIS1316 4.7 58.7 1.0
C B:CYS1317 4.8 58.6 1.0
CA B:CYS1287 4.8 38.2 1.0
C B:CYS1290 4.8 51.6 1.0
ND1 B:HIS1316 4.8 62.7 1.0
N B:ASP1291 4.9 48.5 1.0
C B:SER1289 4.9 52.3 1.0
N B:GLU1318 5.0 56.9 1.0

Zinc binding site 2 out of 8 in 3flo

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Zinc binding site 2 out of 8 in the Crystal Structure of the Carboxyl-Terminal Domain of Yeast Dna Polymerase Alpha in Complex with Its B 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 the Carboxyl-Terminal Domain of Yeast Dna Polymerase Alpha in Complex with Its B Subunit within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn2

b:63.8
occ:1.00
 SG B:CYS1367 2.3 56.8 1.0
SG B:CYS1348 2.4 61.7 1.0
SG B:CYS1353 2.4 68.4 1.0
SG B:CYS1372 2.4 72.0 1.0
CB B:CYS1348 3.3 56.1 1.0
CB B:CYS1353 3.3 72.1 1.0
CB B:CYS1367 3.4 57.1 1.0
CB B:CYS1372 3.5 71.7 1.0
CB B:ASP1350 4.5 75.9 1.0
CA B:CYS1348 4.7 54.0 1.0
N B:GLY1374 4.7 68.3 1.0
CA B:GLY1374 4.7 65.5 1.0
CB B:ASN1369 4.7 69.1 1.0
N B:GLY1354 4.7 64.9 1.0
CA B:CYS1353 4.8 72.6 1.0
CA B:CYS1367 4.8 53.5 1.0
CA B:CYS1372 4.8 75.8 1.0
CG1 B:ILE1355 4.9 52.5 1.0

Zinc binding site 3 out of 8 in 3flo

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Zinc binding site 3 out of 8 in the Crystal Structure of the Carboxyl-Terminal Domain of Yeast Dna Polymerase Alpha in Complex with Its B 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 the Carboxyl-Terminal Domain of Yeast Dna Polymerase Alpha in Complex with Its B Subunit within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn1

b:70.1
occ:1.00
 SG D:CYS1314 2.3 0.0 1.0
SG D:CYS1290 2.4 0.9 1.0
SG D:CYS1287 2.4 91.4 1.0
SG D:CYS1317 2.4 0.0 1.0
CB D:CYS1287 3.2 87.6 1.0
CB D:CYS1314 3.3 96.5 1.0
CB D:CYS1290 3.4 0.2 1.0
CB D:CYS1317 3.5 0.2 1.0
N D:CYS1290 3.9 98.7 1.0
N D:CYS1317 3.9 0.7 1.0
CA D:CYS1290 4.2 0.2 1.0
CA D:CYS1317 4.3 0.6 1.0
CB D:HIS1316 4.5 0.9 1.0
CA D:CYS1287 4.7 81.5 1.0
CA D:CYS1314 4.7 98.4 1.0
C D:CYS1290 4.7 0.2 1.0
CB D:SER1289 4.8 95.5 1.0
N D:ASP1291 4.8 97.5 1.0
C D:HIS1316 4.9 0.5 1.0
C D:CYS1317 5.0 0.1 1.0
C D:SER1289 5.0 97.6 1.0

Zinc binding site 4 out of 8 in 3flo

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Zinc binding site 4 out of 8 in the Crystal Structure of the Carboxyl-Terminal Domain of Yeast Dna Polymerase Alpha in Complex with Its B 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 the Carboxyl-Terminal Domain of Yeast Dna Polymerase Alpha in Complex with Its B Subunit within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn2

b:66.0
occ:1.00
 SG D:CYS1367 2.3 65.9 1.0
SG D:CYS1348 2.3 73.6 1.0
SG D:CYS1372 2.4 80.2 1.0
SG D:CYS1353 2.4 83.7 1.0
CB D:CYS1348 3.3 69.1 1.0
CB D:CYS1367 3.3 61.6 1.0
CB D:CYS1353 3.4 89.5 1.0
CB D:CYS1372 3.4 78.0 1.0
CB D:ASN1369 4.5 79.8 1.0
CB D:ASP1350 4.6 88.6 1.0
N D:GLY1374 4.7 71.4 1.0
CA D:CYS1367 4.7 57.1 1.0
CA D:CYS1348 4.7 67.2 1.0
CA D:GLY1374 4.8 70.4 1.0
N D:GLY1354 4.8 86.2 1.0
CA D:CYS1372 4.8 79.1 1.0
CG1 D:ILE1355 4.8 68.7 1.0
CA D:CYS1353 4.8 93.9 1.0
OD1 D:ASN1369 5.0 85.7 1.0

Zinc binding site 5 out of 8 in 3flo

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Zinc binding site 5 out of 8 in the Crystal Structure of the Carboxyl-Terminal Domain of Yeast Dna Polymerase Alpha in Complex with Its B 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 the Carboxyl-Terminal Domain of Yeast Dna Polymerase Alpha in Complex with Its B Subunit within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn1

b:72.1
occ:1.00
 SG F:CYS1317 2.3 0.9 1.0
SG F:CYS1287 2.4 0.1 1.0
SG F:CYS1314 2.4 0.7 1.0
SG F:CYS1290 2.4 0.7 1.0
CB F:CYS1314 3.1 0.3 1.0
CB F:CYS1317 3.4 0.0 1.0
CB F:CYS1287 3.4 0.2 1.0
CB F:CYS1290 3.5 0.9 1.0
N F:CYS1317 3.7 0.9 1.0
CA F:CYS1317 4.1 0.8 1.0
N F:CYS1290 4.2 0.4 1.0
CA F:CYS1314 4.4 0.7 1.0
CA F:CYS1290 4.5 0.6 1.0
C F:CYS1317 4.6 0.2 1.0
CB F:HIS1316 4.6 0.8 1.0
CB F:SER1289 4.6 0.7 1.0
O F:CYS1314 4.7 0.2 1.0
C F:CYS1314 4.7 0.6 1.0
N F:GLU1318 4.7 0.3 1.0
CB F:GLN1319 4.7 0.8 1.0
N F:GLN1319 4.7 0.6 1.0
C F:HIS1316 4.8 0.7 1.0
CA F:CYS1287 4.8 0.7 1.0
N F:HIS1316 5.0 0.1 1.0

Zinc binding site 6 out of 8 in 3flo

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Zinc binding site 6 out of 8 in the Crystal Structure of the Carboxyl-Terminal Domain of Yeast Dna Polymerase Alpha in Complex with Its B 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 the Carboxyl-Terminal Domain of Yeast Dna Polymerase Alpha in Complex with Its B Subunit within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn2

b:68.4
occ:1.00
 SG F:CYS1372 2.3 0.8 1.0
SG F:CYS1348 2.3 0.0 1.0
SG F:CYS1367 2.4 96.4 1.0
SG F:CYS1353 2.4 0.8 1.0
CB F:CYS1367 3.3 90.7 1.0
CB F:CYS1348 3.3 99.2 1.0
CB F:CYS1372 3.4 0.3 1.0
CB F:CYS1353 3.4 1.0 1.0
CB F:ASN1369 4.4 0.4 1.0
CB F:ASP1350 4.7 0.0 1.0
CA F:CYS1367 4.7 84.9 1.0
N F:GLY1374 4.7 99.0 1.0
CA F:GLY1374 4.7 97.1 1.0
CA F:CYS1348 4.7 95.6 1.0
CA F:CYS1372 4.8 0.2 1.0
N F:GLY1354 4.8 1.0 1.0
CA F:CYS1353 4.8 0.6 1.0
CG1 F:ILE1355 4.9 0.0 1.0

Zinc binding site 7 out of 8 in 3flo

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Zinc binding site 7 out of 8 in the Crystal Structure of the Carboxyl-Terminal Domain of Yeast Dna Polymerase Alpha in Complex with Its B 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 the Carboxyl-Terminal Domain of Yeast Dna Polymerase Alpha in Complex with Its B Subunit within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Zn1

b:68.0
occ:1.00
 SG H:CYS1290 2.3 92.3 1.0
SG H:CYS1314 2.4 86.2 1.0
SG H:CYS1287 2.4 77.0 1.0
SG H:CYS1317 2.4 92.3 1.0
CB H:CYS1287 3.3 74.2 1.0
CB H:CYS1290 3.3 93.7 1.0
CB H:CYS1314 3.4 81.3 1.0
CB H:CYS1317 3.4 98.0 1.0
N H:CYS1290 3.8 85.1 1.0
N H:CYS1317 3.9 0.9 1.0
CA H:CYS1290 4.1 90.2 1.0
CA H:CYS1317 4.2 0.7 1.0
CB H:SER1289 4.6 81.6 1.0
CB H:HIS1316 4.6 0.5 1.0
CA H:CYS1287 4.7 68.9 1.0
C H:CYS1290 4.7 89.5 1.0
CA H:CYS1314 4.8 82.2 1.0
N H:ASP1291 4.8 84.4 1.0
ND1 H:HIS1316 4.8 0.5 1.0
C H:SER1289 4.9 83.9 1.0
C H:HIS1316 4.9 0.2 1.0
C H:CYS1317 4.9 98.1 1.0

Zinc binding site 8 out of 8 in 3flo

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Zinc binding site 8 out of 8 in the Crystal Structure of the Carboxyl-Terminal Domain of Yeast Dna Polymerase Alpha in Complex with Its B 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 the Carboxyl-Terminal Domain of Yeast Dna Polymerase Alpha in Complex with Its B Subunit within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Zn2

b:61.8
occ:1.00
 SG H:CYS1348 2.3 59.4 1.0
SG H:CYS1353 2.3 69.7 1.0
SG H:CYS1372 2.3 66.5 1.0
SG H:CYS1367 2.4 53.5 1.0
CB H:CYS1367 3.3 50.3 1.0
CB H:CYS1353 3.3 75.0 1.0
CB H:CYS1372 3.4 64.3 1.0
CB H:CYS1348 3.4 57.8 1.0
CB H:ASN1369 4.6 66.8 1.0
CB H:ASP1350 4.6 74.3 1.0
CA H:CYS1372 4.7 64.8 1.0
N H:GLY1374 4.7 58.1 1.0
CA H:CYS1367 4.8 46.4 1.0
CA H:CYS1353 4.8 79.2 1.0
N H:GLY1354 4.8 72.6 1.0
CA H:GLY1374 4.8 57.3 1.0
CA H:CYS1348 4.8 56.3 1.0
CD1 H:ILE1355 4.9 57.8 1.0
CG1 H:ILE1355 4.9 57.2 1.0
C H:CYS1372 5.0 61.6 1.0

Reference:

S.Klinge, R.Nunez-Ramirez, O.Llorca, L.Pellegrini. 3D Architecture of Dna Pol Alpha Reveals the Functional Core of Multi-Subunit Replicative Polymerases Embo J. V. 28 1978 2009.
ISSN: ISSN 0261-4189
PubMed: 19494830
DOI: 10.1038/EMBOJ.2009.150
Page generated: Thu Oct 24 13:17:25 2024

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