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:
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
Go back to
Zinc Binding Sites List in 5exr
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
Go back to
Zinc Binding Sites List in 5exr
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
Go back to
Zinc Binding Sites List in 5exr
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
Go back to
Zinc Binding Sites List in 5exr
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: Sun Oct 27 15:35:20 2024
|