Sodium in PDB 4pvh: Engineered Oxidase Reveals Steric Control of Oxygen Reduction
Protein crystallography data
The structure of Engineered Oxidase Reveals Steric Control of Oxygen Reduction, PDB code: 4pvh
was solved by
D.Zafred,
A.Teufelberger,
W.Keller,
P.Macheroux,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
45.56 /
1.40
|
Space group
|
P 61 2 2
|
Cell size a, b, c (Å), α, β, γ (°)
|
118.040,
118.040,
201.110,
90.00,
90.00,
120.00
|
R / Rfree (%)
|
14.4 /
16.7
|
Sodium Binding Sites:
The binding sites of Sodium atom in the Engineered Oxidase Reveals Steric Control of Oxygen Reduction
(pdb code 4pvh). This binding sites where shown within
5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the
Engineered Oxidase Reveals Steric Control of Oxygen Reduction, PDB code: 4pvh:
Jump to Sodium binding site number:
1;
2;
Sodium binding site 1 out
of 2 in 4pvh
Go back to
Sodium Binding Sites List in 4pvh
Sodium binding site 1 out
of 2 in the Engineered Oxidase Reveals Steric Control of Oxygen Reduction
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 1 of Engineered Oxidase Reveals Steric Control of Oxygen Reduction within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na602
b:16.7
occ:1.00
|
OE2
|
A:GLU89
|
2.3
|
14.8
|
1.0
|
O
|
A:HOH820
|
2.3
|
23.5
|
1.0
|
OE1
|
A:GLU338
|
2.3
|
16.2
|
1.0
|
O
|
A:HOH716
|
2.4
|
14.5
|
1.0
|
O
|
A:HOH749
|
2.4
|
18.1
|
1.0
|
O
|
A:HOH729
|
2.6
|
16.2
|
1.0
|
CD
|
A:GLU89
|
3.1
|
13.6
|
1.0
|
HH12
|
A:ARG44
|
3.3
|
23.8
|
1.0
|
CD
|
A:GLU338
|
3.3
|
16.7
|
1.0
|
OE1
|
A:GLU89
|
3.4
|
15.2
|
1.0
|
OE2
|
A:GLU338
|
3.6
|
19.8
|
1.0
|
HA
|
A:ASP441
|
3.6
|
14.5
|
1.0
|
H
|
A:TYR339
|
3.7
|
15.7
|
1.0
|
H
|
A:ILE442
|
3.7
|
15.8
|
1.0
|
HG22
|
A:ILE442
|
3.9
|
18.1
|
1.0
|
O
|
A:HOH1294
|
4.0
|
36.2
|
1.0
|
HA
|
A:GLU338
|
4.0
|
16.1
|
1.0
|
NH1
|
A:ARG44
|
4.1
|
19.8
|
1.0
|
HZ2
|
A:TRP45
|
4.2
|
19.3
|
1.0
|
O
|
A:TYR339
|
4.3
|
14.3
|
1.0
|
HG2
|
A:GLU89
|
4.3
|
15.3
|
1.0
|
OD1
|
A:ASP441
|
4.3
|
14.2
|
1.0
|
CG
|
A:GLU89
|
4.4
|
12.8
|
1.0
|
HH11
|
A:ARG44
|
4.4
|
23.8
|
1.0
|
HH22
|
A:ARG44
|
4.4
|
26.5
|
1.0
|
N
|
A:ILE442
|
4.5
|
13.1
|
1.0
|
N
|
A:TYR339
|
4.6
|
13.1
|
1.0
|
O
|
A:ARG440
|
4.6
|
12.6
|
1.0
|
CA
|
A:ASP441
|
4.6
|
12.1
|
1.0
|
O
|
A:HOH1142
|
4.6
|
35.1
|
1.0
|
O
|
A:HOH1163
|
4.7
|
48.5
|
1.0
|
CG
|
A:GLU338
|
4.7
|
14.8
|
1.0
|
HD2
|
A:TYR339
|
4.8
|
16.6
|
1.0
|
CG2
|
A:ILE442
|
4.8
|
15.1
|
1.0
|
OD2
|
A:ASP443
|
4.8
|
28.1
|
1.0
|
H
|
A:ASP443
|
4.8
|
15.5
|
1.0
|
HG3
|
A:GLU89
|
4.8
|
15.3
|
1.0
|
CA
|
A:GLU338
|
4.9
|
13.4
|
1.0
|
HB3
|
A:TYR88
|
4.9
|
15.4
|
1.0
|
HB2
|
A:GLU338
|
4.9
|
17.8
|
1.0
|
O
|
A:TYR88
|
5.0
|
12.4
|
1.0
|
HA
|
A:GLU89
|
5.0
|
14.8
|
1.0
|
CG
|
A:ASP441
|
5.0
|
12.8
|
1.0
|
|
Sodium binding site 2 out
of 2 in 4pvh
Go back to
Sodium Binding Sites List in 4pvh
Sodium binding site 2 out
of 2 in the Engineered Oxidase Reveals Steric Control of Oxygen Reduction
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 2 of Engineered Oxidase Reveals Steric Control of Oxygen Reduction within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na603
b:28.3
occ:1.00
|
O
|
A:LYS430
|
2.2
|
21.8
|
1.0
|
O
|
A:HOH1299
|
2.3
|
33.3
|
1.0
|
O
|
A:HOH1002
|
2.3
|
32.5
|
1.0
|
O
|
A:HOH1086
|
2.4
|
34.6
|
1.0
|
O
|
A:HOH1298
|
2.4
|
24.0
|
1.0
|
O
|
A:HOH777
|
2.4
|
17.9
|
1.0
|
HZ1
|
A:LYS468
|
3.1
|
22.4
|
0.4
|
H
|
A:LYS430
|
3.2
|
21.5
|
1.0
|
HZ3
|
A:LYS468
|
3.3
|
22.4
|
0.4
|
C
|
A:LYS430
|
3.4
|
19.1
|
1.0
|
NZ
|
A:LYS468
|
3.6
|
18.7
|
0.4
|
O
|
A:ASN431
|
3.7
|
21.2
|
1.0
|
HB2
|
A:ASN431
|
3.8
|
27.6
|
1.0
|
N
|
A:LYS430
|
3.9
|
17.9
|
1.0
|
C
|
A:ASN431
|
4.0
|
19.7
|
1.0
|
HZ2
|
A:LYS468
|
4.1
|
22.4
|
0.4
|
HD2
|
A:PRO432
|
4.1
|
21.6
|
1.0
|
HB2
|
A:SER429
|
4.2
|
18.3
|
1.0
|
HG3
|
A:LYS430
|
4.2
|
32.9
|
1.0
|
CA
|
A:LYS430
|
4.2
|
18.9
|
1.0
|
O
|
A:PRO432
|
4.3
|
15.2
|
1.0
|
N
|
A:ASN431
|
4.4
|
20.0
|
1.0
|
N
|
A:PRO432
|
4.4
|
17.4
|
1.0
|
O
|
A:HOH1327
|
4.4
|
47.8
|
1.0
|
HE3
|
A:LYS468
|
4.4
|
21.3
|
0.4
|
CA
|
A:ASN431
|
4.5
|
19.7
|
1.0
|
HE3
|
A:LYS468
|
4.6
|
22.8
|
0.6
|
HG2
|
A:LYS430
|
4.6
|
32.9
|
1.0
|
CB
|
A:ASN431
|
4.6
|
23.0
|
1.0
|
CE
|
A:LYS468
|
4.7
|
17.7
|
0.4
|
CD
|
A:PRO432
|
4.8
|
18.0
|
1.0
|
CG
|
A:LYS430
|
4.8
|
27.4
|
1.0
|
OE1
|
A:GLN434
|
4.8
|
15.9
|
1.0
|
HA
|
A:SER429
|
4.9
|
17.9
|
1.0
|
HZ1
|
A:LYS468
|
5.0
|
18.2
|
0.6
|
HA
|
A:LYS430
|
5.0
|
22.6
|
1.0
|
|
Reference:
D.Zafred,
A.Teufelberger,
W.Keller,
P.Macheroux.
Engineered Oxidase Reveals Steric Control of Oxygen Reduction To Be Published.
Page generated: Mon Oct 7 17:49:17 2024
|