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Zinc in PDB 5exr: Crystal Structure of Human Primosome

Enzymatic activity of Crystal Structure of Human Primosome

All present enzymatic activity of Crystal Structure of Human Primosome:
2.7.7.7;

Protein crystallography data

The structure of Crystal Structure of Human Primosome, PDB code: 5exr was solved by T.H.Tahirov, A.G.Baranovskiy, N.D.Babayeva, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 39.94 / 3.60
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 113.096, 210.164, 172.565, 90.00, 93.56, 90.00
R / Rfree (%) 26.8 / 32.6

Other elements in 5exr:

The structure of Crystal Structure of Human Primosome also contains other interesting chemical elements:

Iron (Fe) 8 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Human Primosome (pdb code 5exr). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the Crystal Structure of Human Primosome, PDB code: 5exr:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 5exr

Go back to Zinc Binding Sites List in 5exr
Zinc binding site 1 out of 6 in the Crystal Structure of Human Primosome


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 Primosome within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn501

b:0.5
occ:1.00
SG A:CYS128 2.3 1.0 1.0
SG A:CYS122 2.3 0.4 1.0
SG A:CYS121 2.3 0.8 1.0
SG A:CYS131 2.3 0.1 1.0
CB A:CYS121 3.4 0.8 1.0
CB A:CYS131 3.4 0.3 1.0
N A:CYS128 3.6 0.1 1.0
CB A:CYS122 3.6 0.2 1.0
N A:CYS131 3.7 0.2 1.0
CB A:CYS128 3.7 98.3 1.0
N A:CYS122 3.8 0.4 1.0
C A:CYS121 4.0 0.5 1.0
CA A:CYS128 4.0 0.2 1.0
O A:CYS128 4.0 98.6 1.0
CA A:CYS131 4.2 0.5 1.0
CA A:CYS122 4.2 0.8 1.0
C A:ILE127 4.2 0.2 1.0
C A:CYS128 4.3 99.7 1.0
CA A:CYS121 4.3 0.2 1.0
C A:LYS130 4.4 0.6 1.0
CB A:LYS130 4.4 99.5 1.0
O A:CYS121 4.5 0.3 1.0
CA A:ILE127 4.5 0.9 1.0
CA A:LYS130 4.6 0.4 1.0
N A:LYS130 4.6 0.5 1.0

Zinc binding site 2 out of 6 in 5exr

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Zinc binding site 2 out of 6 in the Crystal Structure of Human Primosome


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 Primosome within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn1501

b:46.9
occ:1.00
SG C:CYS1310 2.2 68.3 1.0
SG C:CYS1315 2.4 73.1 1.0
SG C:CYS1286 2.4 77.3 1.0
SG C:CYS1283 2.5 64.5 1.0
CB C:CYS1283 2.9 70.9 1.0
CB C:CYS1315 3.3 77.4 1.0
CB C:CYS1310 3.3 76.1 1.0
CB C:CYS1286 3.5 80.1 1.0
N C:CYS1286 3.8 74.7 1.0
CA C:CYS1286 4.2 79.1 1.0
CA C:CYS1283 4.4 62.1 1.0
CB C:ASN1312 4.6 82.1 1.0
CB C:ALA1317 4.6 59.1 1.0
CA C:CYS1310 4.7 77.4 1.0
CA C:CYS1315 4.7 74.9 1.0
N C:GLY1287 4.9 81.2 1.0
CB C:THR1285 4.9 61.9 1.0
C C:THR1285 5.0 67.6 1.0
C C:CYS1283 5.0 55.9 1.0

Zinc binding site 3 out of 6 in 5exr

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Zinc binding site 3 out of 6 in the Crystal Structure of Human Primosome


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 Primosome within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn1502

b:26.7
occ:1.00
SG C:CYS1348 2.2 18.5 1.0
SG C:CYS1371 2.3 1.1 1.0
SG C:CYS1353 2.4 1.5 1.0
CB C:CYS1371 2.9 1.1 1.0
CB C:CYS1348 3.2 40.8 1.0
CB C:CYS1353 3.2 29.6 1.0
CB C:ALA1377 3.3 71.1 1.0
CB C:CYS1374 3.7 46.2 1.0
O C:CYS1374 3.8 57.4 1.0
N C:CYS1374 4.1 51.5 1.0
SG C:CYS1374 4.2 34.1 1.0
CA C:CYS1371 4.3 7.8 1.0
CA C:CYS1348 4.4 39.4 1.0
CA C:CYS1374 4.4 50.1 1.0
O C:ALA1377 4.5 75.3 1.0
CA C:ALA1377 4.5 73.6 1.0
C C:CYS1374 4.6 53.3 1.0
CA C:CYS1353 4.6 36.7 1.0
C C:ALA1377 4.8 72.1 1.0
CB C:ALA1373 4.9 55.6 1.0
N C:ARG1354 4.9 48.8 1.0
N C:ALA1377 4.9 74.2 1.0
CB C:ASN1355 4.9 59.5 1.0
C C:CYS1371 5.0 17.5 1.0

Zinc binding site 4 out of 6 in 5exr

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Zinc binding site 4 out of 6 in the Crystal Structure of Human Primosome


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 Primosome within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn501

b:91.7
occ:1.00
SG E:CYS122 2.3 92.0 1.0
SG E:CYS131 2.3 0.1 1.0
SG E:CYS128 2.3 71.7 1.0
SG E:CYS121 2.3 88.6 1.0
CB E:CYS131 3.1 0.7 1.0
N E:CYS128 3.4 0.6 1.0
CB E:CYS121 3.4 95.6 1.0
CB E:CYS122 3.5 1.0 1.0
CB E:CYS128 3.6 87.9 1.0
O E:CYS128 3.7 99.8 1.0
N E:CYS122 3.8 0.6 1.0
CA E:CYS128 3.9 96.2 1.0
N E:CYS131 3.9 0.5 1.0
C E:CYS121 4.0 0.2 1.0
C E:CYS128 4.1 99.3 1.0
C E:ILE127 4.1 0.2 1.0
CA E:CYS131 4.2 0.7 1.0
CA E:CYS122 4.2 0.1 1.0
CA E:CYS121 4.3 0.3 1.0
C E:LYS130 4.3 1.0 1.0
CA E:ILE127 4.4 0.1 1.0
O E:CYS121 4.5 0.4 1.0
CB E:LYS130 4.6 0.1 1.0
NE E:ARG119 4.7 0.0 1.0
N E:LYS130 4.7 0.6 1.0
CA E:LYS130 4.8 0.5 1.0
O E:LYS130 4.9 0.2 1.0
NE2 E:GLN231 4.9 83.4 1.0

Zinc binding site 5 out of 6 in 5exr

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Zinc binding site 5 out of 6 in the Crystal Structure of Human Primosome


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 Primosome within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Zn1501

b:78.3
occ:1.00
SG G:CYS1310 2.1 71.8 1.0
SG G:CYS1286 2.3 62.4 1.0
SG G:CYS1315 2.8 64.5 1.0
CB G:CYS1315 2.9 73.6 1.0
SG G:CYS1283 3.0 46.5 1.0
CB G:CYS1286 3.1 75.7 1.0
CB G:CYS1310 3.2 72.6 1.0
CB G:CYS1283 3.4 51.1 1.0
CB G:ASN1312 3.5 69.0 1.0
N G:CYS1286 4.1 73.5 1.0
CA G:CYS1286 4.2 76.2 1.0
ND2 G:ASN1312 4.3 79.2 1.0
CG G:ASN1312 4.4 76.7 1.0
CA G:CYS1315 4.4 74.5 1.0
CA G:CYS1310 4.6 72.8 1.0
CA G:ASN1312 4.7 65.4 1.0
N G:ASN1312 4.7 60.9 1.0
C G:CYS1286 4.8 79.1 1.0
N G:GLY1287 4.8 81.2 1.0
CA G:CYS1283 4.9 49.3 1.0
O G:ASN1312 4.9 64.4 1.0

Zinc binding site 6 out of 6 in 5exr

Go back to Zinc Binding Sites List in 5exr
Zinc binding site 6 out of 6 in the Crystal Structure of Human Primosome


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 Primosome within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Zn1502

b:1.1
occ:1.00
SG G:CYS1348 2.0 27.1 1.0
SG G:CYS1353 2.4 3.0 1.0
SG G:CYS1371 2.4 1.1 1.0
CB G:CYS1353 3.0 11.0 1.0
CB G:CYS1371 3.1 1.1 1.0
CB G:CYS1348 3.1 42.3 1.0
SG G:CYS1374 3.1 41.5 1.0
CB G:ALA1377 3.3 74.0 1.0
CB G:CYS1374 3.7 47.3 1.0
O G:CYS1374 4.0 52.1 1.0
N G:CYS1374 4.2 48.3 1.0
CA G:CYS1348 4.4 33.0 1.0
CA G:CYS1374 4.5 49.5 1.0
CA G:CYS1353 4.5 21.3 1.0
CA G:CYS1371 4.5 3.3 1.0
CA G:ALA1377 4.6 75.6 1.0
O G:ALA1377 4.6 79.7 1.0
C G:CYS1374 4.7 50.0 1.0
N G:ARG1354 4.8 32.3 1.0
C G:ALA1377 4.8 73.7 1.0
C G:CYS1353 4.9 27.5 1.0
CB G:GLU1350 4.9 37.1 1.0
CB G:ASN1355 4.9 53.4 1.0
N G:ALA1377 5.0 75.3 1.0
CB G:ALA1373 5.0 44.9 1.0
N G:ASN1355 5.0 45.2 1.0

Reference:

A.G.Baranovskiy, N.D.Babayeva, Y.Zhang, J.Gu, Y.Suwa, Y.I.Pavlov, T.H.Tahirov. Mechanism of Concerted Rna-Dna Primer Synthesis By the Human Primosome. J.Biol.Chem. V. 291 10006 2016.
ISSN: ESSN 1083-351X
PubMed: 26975377
DOI: 10.1074/JBC.M116.717405
Page generated: Wed Dec 16 06:10:45 2020

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