Sodium in PDB 8pjd: Crystal Structure of Mus Musculus Protein Arginine Methyltransferase 2 94-445
Protein crystallography data
The structure of Crystal Structure of Mus Musculus Protein Arginine Methyltransferase 2 94-445, PDB code: 8pjd
was solved by
V.Cura,
N.Troffer-Charlier,
N.Marechal,
L.Bonnefond,
J.Cavarelli,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
29.25 /
1.60
|
Space group
|
C 2 2 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
65.052,
115.98,
133.718,
90,
90,
90
|
R / Rfree (%)
|
17.1 /
18.9
|
Sodium Binding Sites:
The binding sites of Sodium atom in the Crystal Structure of Mus Musculus Protein Arginine Methyltransferase 2 94-445
(pdb code 8pjd). This binding sites where shown within
5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the
Crystal Structure of Mus Musculus Protein Arginine Methyltransferase 2 94-445, PDB code: 8pjd:
Jump to Sodium binding site number:
1;
2;
Sodium binding site 1 out
of 2 in 8pjd
Go back to
Sodium Binding Sites List in 8pjd
Sodium binding site 1 out
of 2 in the Crystal Structure of Mus Musculus Protein Arginine Methyltransferase 2 94-445
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 1 of Crystal Structure of Mus Musculus Protein Arginine Methyltransferase 2 94-445 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na506
b:34.6
occ:1.00
|
OXT
|
A:ACT504
|
2.5
|
28.4
|
1.0
|
O
|
A:LYS383
|
2.6
|
24.4
|
1.0
|
HA
|
A:GLN384
|
2.6
|
25.5
|
1.0
|
HA
|
A:TRP354
|
2.7
|
26.5
|
1.0
|
OG1
|
A:THR373
|
2.8
|
20.8
|
1.0
|
HB
|
A:THR373
|
2.9
|
26.2
|
1.0
|
HB2
|
A:TRP354
|
3.0
|
26.6
|
1.0
|
H1
|
A:ACT504
|
3.0
|
37.0
|
1.0
|
H2
|
A:ACT504
|
3.0
|
37.0
|
1.0
|
C
|
A:ACT504
|
3.2
|
23.8
|
1.0
|
CH3
|
A:ACT504
|
3.2
|
30.9
|
1.0
|
HB3
|
A:TRP354
|
3.3
|
26.6
|
1.0
|
HG3
|
A:GLN384
|
3.3
|
29.1
|
1.0
|
CB
|
A:THR373
|
3.3
|
21.9
|
1.0
|
HB3
|
A:TRP382
|
3.4
|
29.1
|
1.0
|
CB
|
A:TRP354
|
3.4
|
22.2
|
1.0
|
CA
|
A:TRP354
|
3.5
|
22.1
|
1.0
|
O
|
A:THR373
|
3.5
|
23.0
|
1.0
|
C
|
A:LYS383
|
3.5
|
23.5
|
1.0
|
CA
|
A:GLN384
|
3.5
|
21.3
|
1.0
|
H
|
A:PHE355
|
3.7
|
28.3
|
1.0
|
HB2
|
A:TRP382
|
3.8
|
29.1
|
1.0
|
N
|
A:GLN384
|
3.9
|
23.5
|
1.0
|
O
|
A:TRP382
|
4.0
|
23.7
|
1.0
|
O
|
A:ALA353
|
4.0
|
20.9
|
1.0
|
CB
|
A:TRP382
|
4.0
|
24.3
|
1.0
|
CG
|
A:GLN384
|
4.2
|
24.3
|
1.0
|
HG21
|
A:THR373
|
4.2
|
26.6
|
1.0
|
H3
|
A:ACT504
|
4.2
|
37.0
|
1.0
|
C
|
A:THR373
|
4.2
|
22.0
|
1.0
|
C
|
A:TRP382
|
4.3
|
22.7
|
1.0
|
N
|
A:PHE355
|
4.3
|
23.6
|
1.0
|
O
|
A:ACT504
|
4.3
|
31.4
|
1.0
|
CB
|
A:GLN384
|
4.4
|
22.9
|
1.0
|
NA
|
A:NA507
|
4.4
|
27.5
|
1.0
|
CG2
|
A:THR373
|
4.4
|
22.2
|
1.0
|
H
|
A:THR385
|
4.4
|
25.3
|
1.0
|
CA
|
A:THR373
|
4.4
|
21.6
|
1.0
|
C
|
A:TRP354
|
4.4
|
21.5
|
1.0
|
C
|
A:GLN384
|
4.5
|
22.2
|
1.0
|
O
|
A:HOH733
|
4.5
|
21.5
|
1.0
|
N
|
A:TRP354
|
4.6
|
23.7
|
1.0
|
HB3
|
A:GLN384
|
4.6
|
27.4
|
1.0
|
N
|
A:LYS383
|
4.6
|
21.5
|
1.0
|
HE21
|
A:GLN384
|
4.6
|
27.1
|
1.0
|
C
|
A:ALA353
|
4.7
|
20.6
|
1.0
|
N
|
A:THR385
|
4.7
|
21.1
|
1.0
|
CA
|
A:LYS383
|
4.7
|
22.3
|
1.0
|
HG2
|
A:GLN384
|
4.7
|
29.1
|
1.0
|
H
|
A:GLN384
|
4.8
|
28.2
|
1.0
|
HD2
|
A:PHE355
|
4.8
|
32.0
|
1.0
|
CG
|
A:TRP354
|
4.8
|
20.6
|
1.0
|
CA
|
A:TRP382
|
4.8
|
21.6
|
1.0
|
HG1
|
A:THR380
|
4.9
|
26.7
|
1.0
|
HA
|
A:THR373
|
5.0
|
25.9
|
1.0
|
HG23
|
A:THR373
|
5.0
|
26.6
|
1.0
|
|
Sodium binding site 2 out
of 2 in 8pjd
Go back to
Sodium Binding Sites List in 8pjd
Sodium binding site 2 out
of 2 in the Crystal Structure of Mus Musculus Protein Arginine Methyltransferase 2 94-445
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 2 of Crystal Structure of Mus Musculus Protein Arginine Methyltransferase 2 94-445 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na507
b:27.5
occ:1.00
|
OXT
|
A:ACT504
|
2.3
|
28.4
|
1.0
|
O
|
A:TRP382
|
2.3
|
23.7
|
1.0
|
O
|
A:SER302
|
2.4
|
26.2
|
1.0
|
O
|
A:HOH834
|
2.5
|
29.5
|
1.0
|
OG1
|
A:THR385
|
2.5
|
29.8
|
1.0
|
HG1
|
A:THR385
|
2.9
|
35.7
|
1.0
|
C
|
A:ACT504
|
3.1
|
23.8
|
1.0
|
HB2
|
A:SER302
|
3.2
|
31.9
|
1.0
|
O
|
A:GLN384
|
3.2
|
25.0
|
1.0
|
O
|
A:ACT504
|
3.3
|
31.4
|
1.0
|
HA
|
A:SER302
|
3.3
|
28.5
|
1.0
|
C
|
A:GLN384
|
3.4
|
22.2
|
1.0
|
C
|
A:SER302
|
3.4
|
28.1
|
1.0
|
C
|
A:TRP382
|
3.5
|
22.7
|
1.0
|
CA
|
A:SER302
|
3.7
|
23.8
|
1.0
|
N
|
A:THR385
|
3.8
|
21.1
|
1.0
|
HB3
|
A:TRP382
|
3.8
|
29.1
|
1.0
|
HA
|
A:GLN384
|
3.8
|
25.5
|
1.0
|
HA
|
A:THR385
|
3.8
|
25.3
|
1.0
|
CB
|
A:THR385
|
3.8
|
24.4
|
1.0
|
CB
|
A:SER302
|
3.9
|
26.6
|
1.0
|
N
|
A:GLN384
|
3.9
|
23.5
|
1.0
|
HG23
|
A:THR227
|
3.9
|
31.2
|
1.0
|
CA
|
A:GLN384
|
3.9
|
21.3
|
1.0
|
HB2
|
A:LYS383
|
4.0
|
30.4
|
1.0
|
CA
|
A:THR385
|
4.0
|
21.1
|
1.0
|
HA
|
A:TRP382
|
4.1
|
25.9
|
1.0
|
H
|
A:GLN384
|
4.1
|
28.2
|
1.0
|
C
|
A:LYS383
|
4.2
|
23.5
|
1.0
|
O
|
A:HOH835
|
4.2
|
36.4
|
1.0
|
H
|
A:THR385
|
4.2
|
25.3
|
1.0
|
CA
|
A:TRP382
|
4.3
|
21.6
|
1.0
|
HB
|
A:THR385
|
4.3
|
29.3
|
1.0
|
HA
|
A:THR227
|
4.4
|
28.8
|
1.0
|
NA
|
A:NA506
|
4.4
|
34.6
|
1.0
|
HB3
|
A:SER302
|
4.4
|
31.9
|
1.0
|
HA
|
A:ASN303
|
4.5
|
31.5
|
1.0
|
CH3
|
A:ACT504
|
4.5
|
30.9
|
1.0
|
CB
|
A:TRP382
|
4.5
|
24.3
|
1.0
|
N
|
A:LYS383
|
4.5
|
21.5
|
1.0
|
N
|
A:ASN303
|
4.6
|
26.0
|
1.0
|
O
|
A:LYS383
|
4.6
|
24.4
|
1.0
|
H2
|
A:ACT504
|
4.7
|
37.0
|
1.0
|
CA
|
A:LYS383
|
4.7
|
22.3
|
1.0
|
CB
|
A:LYS383
|
4.7
|
25.3
|
1.0
|
HG23
|
A:THR385
|
4.7
|
31.3
|
1.0
|
H
|
A:CYS228
|
4.8
|
28.5
|
1.0
|
CG2
|
A:THR385
|
4.8
|
26.1
|
1.0
|
H
|
A:HIS304
|
4.8
|
28.5
|
1.0
|
CG2
|
A:THR227
|
4.8
|
26.0
|
1.0
|
HD1
|
A:TRP382
|
4.9
|
28.4
|
1.0
|
OG
|
A:SER302
|
4.9
|
28.6
|
1.0
|
OG1
|
A:THR227
|
4.9
|
26.6
|
1.0
|
|
Reference:
V.Cura,
N.Troffer-Charlier,
N.Marechal,
L.Bonnefond,
J.Cavarelli.
Crystal Structure of Mus Musculus Protein Arginine Methyltransferase 2 94-445 To Be Published.
Page generated: Wed Oct 9 13:01:10 2024
|