Iron in PDB 4rr2: Crystal Structure of Human Primase
Protein crystallography data
The structure of Crystal Structure of Human Primase, PDB code: 4rr2
was solved by
A.G.Baranovskiy,
J.Gu,
Y.Suwa,
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)
|
48.48 /
2.65
|
Space group
|
P 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
86.195,
88.899,
94.682,
93.82,
96.57,
111.72
|
R / Rfree (%)
|
22.9 /
27.1
|
Other elements in 4rr2:
The structure of Crystal Structure of Human Primase also contains other interesting chemical elements:
Iron Binding Sites:
The binding sites of Iron atom in the Crystal Structure of Human Primase
(pdb code 4rr2). This binding sites where shown within
5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the
Crystal Structure of Human Primase, PDB code: 4rr2:
Jump to Iron binding site number:
1;
2;
3;
4;
Iron binding site 1 out
of 4 in 4rr2
Go back to
Iron Binding Sites List in 4rr2
Iron binding site 1 out
of 4 in the Crystal Structure of Human Primase
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 1 of Crystal Structure of Human Primase within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Fe1000
b:30.9
occ:1.00
|
FE1
|
D:SF41000
|
0.0
|
30.9
|
1.0
|
S3
|
D:SF41000
|
2.1
|
27.6
|
1.0
|
S2
|
D:SF41000
|
2.2
|
19.2
|
1.0
|
S4
|
D:SF41000
|
2.2
|
26.5
|
1.0
|
SG
|
D:CYS367
|
2.4
|
40.2
|
1.0
|
FE2
|
D:SF41000
|
2.9
|
25.4
|
1.0
|
FE3
|
D:SF41000
|
3.0
|
38.4
|
1.0
|
FE4
|
D:SF41000
|
3.1
|
32.3
|
1.0
|
CB
|
D:CYS367
|
3.1
|
36.6
|
1.0
|
CA
|
D:CYS367
|
3.6
|
41.5
|
1.0
|
S1
|
D:SF41000
|
3.6
|
17.7
|
1.0
|
CG
|
D:PRO444
|
4.3
|
22.6
|
1.0
|
CD
|
D:PRO444
|
4.4
|
18.1
|
1.0
|
N
|
D:CYS367
|
4.5
|
39.2
|
1.0
|
C
|
D:CYS367
|
4.7
|
38.8
|
1.0
|
CD2
|
D:LEU441
|
4.7
|
24.1
|
1.0
|
N
|
D:PRO444
|
4.8
|
25.2
|
1.0
|
CG
|
D:GLN421
|
4.9
|
38.7
|
1.0
|
O
|
D:CYS367
|
4.9
|
30.6
|
1.0
|
SG
|
D:CYS384
|
5.0
|
44.8
|
1.0
|
|
Iron binding site 2 out
of 4 in 4rr2
Go back to
Iron Binding Sites List in 4rr2
Iron binding site 2 out
of 4 in the Crystal Structure of Human Primase
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 2 of Crystal Structure of Human Primase within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Fe1000
b:25.4
occ:1.00
|
FE2
|
D:SF41000
|
0.0
|
25.4
|
1.0
|
S4
|
D:SF41000
|
2.1
|
26.5
|
1.0
|
S1
|
D:SF41000
|
2.2
|
17.7
|
1.0
|
S3
|
D:SF41000
|
2.2
|
27.6
|
1.0
|
SG
|
D:CYS384
|
2.3
|
44.8
|
1.0
|
FE1
|
D:SF41000
|
2.9
|
30.9
|
1.0
|
FE3
|
D:SF41000
|
2.9
|
38.4
|
1.0
|
FE4
|
D:SF41000
|
3.1
|
32.3
|
1.0
|
CB
|
D:CYS384
|
3.1
|
38.5
|
1.0
|
S2
|
D:SF41000
|
3.6
|
19.2
|
1.0
|
CA
|
D:CYS384
|
4.0
|
38.7
|
1.0
|
CD2
|
D:PHE386
|
4.4
|
49.0
|
1.0
|
CD
|
D:PRO385
|
4.6
|
26.4
|
1.0
|
SG
|
D:CYS424
|
4.7
|
36.1
|
1.0
|
C
|
D:CYS384
|
4.8
|
34.7
|
1.0
|
CB
|
D:CYS287
|
4.9
|
32.5
|
1.0
|
CG1
|
D:ILE371
|
4.9
|
46.0
|
1.0
|
N
|
D:PRO385
|
4.9
|
31.9
|
1.0
|
|
Iron binding site 3 out
of 4 in 4rr2
Go back to
Iron Binding Sites List in 4rr2
Iron binding site 3 out
of 4 in the Crystal Structure of Human Primase
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 3 of Crystal Structure of Human Primase within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Fe1000
b:38.4
occ:1.00
|
FE3
|
D:SF41000
|
0.0
|
38.4
|
1.0
|
S4
|
D:SF41000
|
2.1
|
26.5
|
1.0
|
S1
|
D:SF41000
|
2.2
|
17.7
|
1.0
|
S2
|
D:SF41000
|
2.2
|
19.2
|
1.0
|
SG
|
D:CYS424
|
2.3
|
36.1
|
1.0
|
FE2
|
D:SF41000
|
2.9
|
25.4
|
1.0
|
FE1
|
D:SF41000
|
3.0
|
30.9
|
1.0
|
FE4
|
D:SF41000
|
3.3
|
32.3
|
1.0
|
CB
|
D:CYS424
|
3.3
|
35.2
|
1.0
|
CD2
|
D:LEU441
|
3.6
|
24.1
|
1.0
|
S3
|
D:SF41000
|
3.8
|
27.6
|
1.0
|
CB
|
D:PRO285
|
4.2
|
30.2
|
1.0
|
CE2
|
D:PHE386
|
4.5
|
46.7
|
1.0
|
CD
|
D:PRO286
|
4.5
|
24.8
|
1.0
|
CD2
|
D:PHE386
|
4.6
|
49.0
|
1.0
|
SG
|
D:CYS367
|
4.6
|
40.2
|
1.0
|
CA
|
D:CYS424
|
4.6
|
30.5
|
1.0
|
CG
|
D:PRO286
|
4.7
|
34.0
|
1.0
|
CG
|
D:LEU441
|
4.8
|
17.9
|
1.0
|
CD1
|
D:PHE447
|
4.9
|
41.7
|
1.0
|
|
Iron binding site 4 out
of 4 in 4rr2
Go back to
Iron Binding Sites List in 4rr2
Iron binding site 4 out
of 4 in the Crystal Structure of Human Primase
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 4 of Crystal Structure of Human Primase within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Fe1000
b:32.3
occ:1.00
|
FE4
|
D:SF41000
|
0.0
|
32.3
|
1.0
|
S3
|
D:SF41000
|
2.1
|
27.6
|
1.0
|
S2
|
D:SF41000
|
2.1
|
19.2
|
1.0
|
S1
|
D:SF41000
|
2.2
|
17.7
|
1.0
|
SG
|
D:CYS287
|
2.4
|
38.4
|
1.0
|
FE1
|
D:SF41000
|
3.1
|
30.9
|
1.0
|
FE2
|
D:SF41000
|
3.1
|
25.4
|
1.0
|
CB
|
D:CYS287
|
3.1
|
32.5
|
1.0
|
FE3
|
D:SF41000
|
3.3
|
38.4
|
1.0
|
CG
|
D:PRO444
|
3.9
|
22.6
|
1.0
|
S4
|
D:SF41000
|
3.9
|
26.5
|
1.0
|
CB
|
D:PRO285
|
4.0
|
30.2
|
1.0
|
N
|
D:CYS287
|
4.0
|
33.4
|
1.0
|
CG
|
D:PRO285
|
4.2
|
35.3
|
1.0
|
CA
|
D:CYS287
|
4.2
|
38.2
|
1.0
|
CB
|
D:PRO444
|
4.5
|
20.2
|
1.0
|
N
|
D:MET288
|
4.9
|
37.3
|
1.0
|
CA
|
D:PRO444
|
5.0
|
27.2
|
1.0
|
CB
|
D:CYS384
|
5.0
|
38.5
|
1.0
|
SG
|
D:CYS384
|
5.0
|
44.8
|
1.0
|
CD
|
D:PRO444
|
5.0
|
18.1
|
1.0
|
|
Reference:
A.G.Baranovskiy,
Y.Zhang,
Y.Suwa,
N.D.Babayeva,
J.Gu,
Y.I.Pavlov,
T.H.Tahirov.
Crystal Structure of the Human Primase. J.Biol.Chem. 2014.
ISSN: ESSN 1083-351X
PubMed: 25550159
DOI: 10.1074/JBC.M114.624742
Page generated: Mon Aug 5 09:24:03 2024
|