Magnesium in PDB 7qow: Crystal Structure of Vibrio Alkaline Phosphatase in 1.0 M Nacl
Protein crystallography data
The structure of Crystal Structure of Vibrio Alkaline Phosphatase in 1.0 M Nacl, PDB code: 7qow
was solved by
S.Markusson,
J.G.Hjorleifsson,
P.Kursula,
B.Asgeirsson,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
43.00 /
1.20
|
Space group
|
P 1 21 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
77.202,
85.993,
85.139,
90,
113.37,
90
|
R / Rfree (%)
|
13.1 /
16
|
Other elements in 7qow:
The structure of Crystal Structure of Vibrio Alkaline Phosphatase in 1.0 M Nacl also contains other interesting chemical elements:
Magnesium Binding Sites:
The binding sites of Magnesium atom in the Crystal Structure of Vibrio Alkaline Phosphatase in 1.0 M Nacl
(pdb code 7qow). This binding sites where shown within
5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the
Crystal Structure of Vibrio Alkaline Phosphatase in 1.0 M Nacl, PDB code: 7qow:
Jump to Magnesium binding site number:
1;
2;
3;
4;
Magnesium binding site 1 out
of 4 in 7qow
Go back to
Magnesium Binding Sites List in 7qow
Magnesium binding site 1 out
of 4 in the Crystal Structure of Vibrio Alkaline Phosphatase in 1.0 M Nacl
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 1 of Crystal Structure of Vibrio Alkaline Phosphatase in 1.0 M Nacl within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg603
b:14.6
occ:1.00
|
OD2
|
A:ASP12
|
2.0
|
14.9
|
1.0
|
OE2
|
A:GLU268
|
2.0
|
14.1
|
1.0
|
O
|
A:HOH888
|
2.1
|
14.8
|
1.0
|
O
|
A:HOH905
|
2.1
|
14.6
|
1.0
|
O
|
A:HOH769
|
2.1
|
14.2
|
1.0
|
OG1
|
A:THR118
|
2.2
|
13.6
|
1.0
|
HG
|
A:SER65
|
3.0
|
21.6
|
0.6
|
CD
|
A:GLU268
|
3.1
|
13.7
|
1.0
|
CG
|
A:ASP12
|
3.1
|
14.0
|
1.0
|
HB
|
A:THR118
|
3.1
|
16.9
|
1.0
|
CB
|
A:THR118
|
3.2
|
14.1
|
1.0
|
HB2
|
A:ASP12
|
3.3
|
15.2
|
1.0
|
H
|
A:THR118
|
3.5
|
17.7
|
1.0
|
OE1
|
A:GLU268
|
3.5
|
14.5
|
1.0
|
CB
|
A:ASP12
|
3.6
|
12.7
|
1.0
|
OG
|
A:SER65
|
3.8
|
16.5
|
0.4
|
OG
|
A:SER65
|
3.8
|
18.0
|
0.6
|
HB3
|
A:ASP12
|
3.9
|
15.2
|
1.0
|
HB3
|
A:SER65
|
3.9
|
17.3
|
0.4
|
HG21
|
A:THR118
|
3.9
|
18.1
|
1.0
|
ND1
|
A:HIS116
|
4.1
|
15.8
|
1.0
|
HA2
|
A:GLY270
|
4.1
|
17.2
|
1.0
|
N
|
A:THR118
|
4.1
|
14.8
|
1.0
|
CG2
|
A:THR118
|
4.1
|
15.1
|
1.0
|
OD1
|
A:ASP12
|
4.2
|
14.3
|
1.0
|
HB2
|
A:SER65
|
4.2
|
19.3
|
0.6
|
HA3
|
A:GLY270
|
4.2
|
17.2
|
1.0
|
HG23
|
A:THR112
|
4.2
|
19.4
|
1.0
|
HB3
|
A:SER65
|
4.2
|
19.3
|
0.6
|
CA
|
A:THR118
|
4.3
|
14.9
|
1.0
|
CB
|
A:SER65
|
4.3
|
16.1
|
0.6
|
CB
|
A:SER65
|
4.4
|
14.5
|
0.4
|
CG
|
A:GLU268
|
4.4
|
14.1
|
1.0
|
O1
|
A:PO4604
|
4.4
|
16.0
|
1.0
|
HG3
|
A:GLU268
|
4.4
|
16.9
|
1.0
|
O
|
A:GLY270
|
4.5
|
14.5
|
1.0
|
HD2
|
A:PRO119
|
4.6
|
18.1
|
1.0
|
HG23
|
A:THR118
|
4.6
|
18.1
|
1.0
|
CA
|
A:GLY270
|
4.6
|
14.4
|
1.0
|
HB3
|
A:HIS116
|
4.6
|
17.5
|
1.0
|
HE1
|
A:HIS116
|
4.6
|
18.3
|
1.0
|
HB3
|
A:ALA117
|
4.7
|
19.1
|
1.0
|
CE1
|
A:HIS116
|
4.7
|
15.3
|
1.0
|
HA
|
A:THR118
|
4.7
|
17.8
|
1.0
|
ZN
|
A:ZN602
|
4.7
|
15.4
|
1.0
|
HB2
|
A:SER65
|
4.7
|
17.3
|
0.4
|
HG2
|
A:GLU268
|
4.7
|
16.9
|
1.0
|
OD2
|
A:ASP315
|
4.8
|
14.8
|
1.0
|
HD3
|
A:PRO119
|
4.8
|
18.1
|
1.0
|
OG1
|
A:THR112
|
4.9
|
15.0
|
1.0
|
HG22
|
A:THR118
|
4.9
|
18.1
|
1.0
|
H
|
A:ALA117
|
5.0
|
17.8
|
1.0
|
|
Magnesium binding site 2 out
of 4 in 7qow
Go back to
Magnesium Binding Sites List in 7qow
Magnesium binding site 2 out
of 4 in the Crystal Structure of Vibrio Alkaline Phosphatase in 1.0 M Nacl
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 2 of Crystal Structure of Vibrio Alkaline Phosphatase in 1.0 M Nacl within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg613
b:16.9
occ:1.00
|
O
|
B:SER485
|
2.2
|
14.9
|
1.0
|
O
|
A:GLY48
|
2.3
|
16.2
|
1.0
|
O
|
A:ALA45
|
2.4
|
15.6
|
1.0
|
O
|
A:GLN46
|
2.4
|
16.5
|
1.0
|
O
|
B:HOH1436
|
2.4
|
23.5
|
1.0
|
C
|
A:GLN46
|
3.1
|
15.8
|
1.0
|
O
|
B:HOH1588
|
3.1
|
31.5
|
1.0
|
HA
|
A:GLN46
|
3.1
|
18.6
|
1.0
|
HB3
|
B:LYS486
|
3.1
|
18.8
|
1.0
|
C
|
A:GLY48
|
3.2
|
16.0
|
1.0
|
C
|
B:SER485
|
3.4
|
14.7
|
1.0
|
HA
|
A:VAL49
|
3.5
|
18.0
|
1.0
|
C
|
A:ALA45
|
3.5
|
15.0
|
1.0
|
CA
|
A:GLN46
|
3.6
|
15.5
|
1.0
|
HA
|
B:LYS486
|
3.7
|
17.4
|
1.0
|
HB3
|
B:SER485
|
3.8
|
18.0
|
1.0
|
N
|
A:GLY48
|
3.8
|
15.9
|
1.0
|
O
|
A:HOH960
|
3.8
|
21.3
|
1.0
|
H
|
A:GLY48
|
3.8
|
19.1
|
1.0
|
CB
|
B:LYS486
|
3.9
|
15.7
|
1.0
|
C
|
A:GLU47
|
4.0
|
16.9
|
1.0
|
N
|
A:GLN46
|
4.0
|
15.6
|
1.0
|
N
|
A:GLU47
|
4.0
|
15.8
|
1.0
|
N
|
A:VAL49
|
4.1
|
15.3
|
1.0
|
CA
|
B:LYS486
|
4.1
|
14.6
|
1.0
|
CA
|
A:GLY48
|
4.1
|
16.1
|
1.0
|
N
|
B:LYS486
|
4.2
|
14.8
|
1.0
|
CA
|
A:VAL49
|
4.2
|
15.0
|
1.0
|
HB2
|
B:LYS486
|
4.2
|
18.8
|
1.0
|
HG12
|
A:VAL49
|
4.3
|
19.1
|
1.0
|
CA
|
B:SER485
|
4.4
|
14.1
|
1.0
|
O
|
A:GLU47
|
4.5
|
17.9
|
1.0
|
CB
|
B:SER485
|
4.5
|
15.0
|
1.0
|
CA
|
A:GLU47
|
4.5
|
16.8
|
1.0
|
HG3
|
A:GLN46
|
4.6
|
28.4
|
1.0
|
HA
|
A:GLU47
|
4.6
|
20.1
|
1.0
|
H
|
A:GLU47
|
4.7
|
18.9
|
1.0
|
HA2
|
A:GLY48
|
4.7
|
19.2
|
1.0
|
HA
|
A:ALA45
|
4.8
|
17.6
|
1.0
|
CA
|
A:ALA45
|
4.8
|
14.7
|
1.0
|
HA3
|
A:GLY48
|
4.8
|
19.2
|
1.0
|
O
|
B:LEU482
|
4.8
|
16.3
|
1.0
|
H
|
B:SER485
|
4.8
|
17.7
|
1.0
|
H
|
A:VAL49
|
4.9
|
18.3
|
1.0
|
H
|
A:GLN46
|
4.9
|
18.7
|
1.0
|
OG
|
B:SER485
|
4.9
|
14.7
|
1.0
|
HG13
|
A:ILE50
|
4.9
|
19.0
|
1.0
|
N
|
B:SER485
|
4.9
|
14.8
|
1.0
|
CB
|
A:GLN46
|
5.0
|
18.4
|
1.0
|
HG13
|
A:VAL49
|
5.0
|
19.1
|
1.0
|
H
|
B:LYS486
|
5.0
|
17.8
|
1.0
|
|
Magnesium binding site 3 out
of 4 in 7qow
Go back to
Magnesium Binding Sites List in 7qow
Magnesium binding site 3 out
of 4 in the Crystal Structure of Vibrio Alkaline Phosphatase in 1.0 M Nacl
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 3 of Crystal Structure of Vibrio Alkaline Phosphatase in 1.0 M Nacl within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg1109
b:15.3
occ:1.00
|
OD2
|
B:ASP12
|
2.0
|
15.8
|
1.0
|
OE2
|
B:GLU268
|
2.0
|
14.6
|
1.0
|
O
|
B:HOH1327
|
2.1
|
15.2
|
1.0
|
O
|
B:HOH1398
|
2.1
|
15.5
|
1.0
|
O
|
B:HOH1262
|
2.1
|
16.0
|
1.0
|
OG1
|
B:THR118
|
2.1
|
14.7
|
1.0
|
HG
|
B:SER65
|
2.9
|
20.4
|
0.5
|
CD
|
B:GLU268
|
3.1
|
14.9
|
1.0
|
HB
|
B:THR118
|
3.1
|
17.9
|
1.0
|
CG
|
B:ASP12
|
3.1
|
15.7
|
1.0
|
CB
|
B:THR118
|
3.2
|
15.0
|
1.0
|
HB2
|
B:ASP12
|
3.2
|
17.7
|
1.0
|
H
|
B:THR118
|
3.4
|
17.7
|
1.0
|
OE1
|
B:GLU268
|
3.4
|
15.9
|
1.0
|
HD1
|
B:HIS116
|
3.5
|
20.0
|
1.0
|
CB
|
B:ASP12
|
3.6
|
14.8
|
1.0
|
OG
|
B:SER65
|
3.8
|
17.0
|
0.5
|
OG
|
B:SER65
|
3.8
|
17.7
|
0.5
|
HB3
|
B:ASP12
|
3.9
|
17.7
|
1.0
|
HG23
|
B:THR118
|
3.9
|
19.0
|
1.0
|
HB3
|
B:SER65
|
4.0
|
19.5
|
0.5
|
HA2
|
B:GLY270
|
4.0
|
18.0
|
1.0
|
O
|
B:HOH1334
|
4.1
|
15.9
|
1.0
|
N
|
B:THR118
|
4.1
|
14.8
|
1.0
|
ND1
|
B:HIS116
|
4.1
|
16.7
|
1.0
|
OD1
|
B:ASP12
|
4.1
|
15.6
|
1.0
|
CG2
|
B:THR118
|
4.1
|
15.8
|
1.0
|
HG23
|
B:THR112
|
4.2
|
19.9
|
1.0
|
HA3
|
B:GLY270
|
4.2
|
18.0
|
1.0
|
CA
|
B:THR118
|
4.2
|
14.7
|
1.0
|
HB2
|
B:SER65
|
4.3
|
18.8
|
0.5
|
HB3
|
B:SER65
|
4.3
|
18.8
|
0.5
|
O
|
B:HOH1201
|
4.3
|
19.6
|
0.6
|
CG
|
B:GLU268
|
4.4
|
15.8
|
1.0
|
CB
|
B:SER65
|
4.4
|
15.7
|
0.5
|
CB
|
B:SER65
|
4.4
|
16.3
|
0.5
|
HG3
|
B:GLU268
|
4.4
|
18.9
|
1.0
|
O2
|
B:PO41104
|
4.4
|
16.5
|
1.0
|
O
|
B:GLY270
|
4.5
|
15.9
|
1.0
|
HD2
|
B:PRO119
|
4.5
|
19.0
|
1.0
|
HG22
|
B:THR118
|
4.6
|
19.0
|
1.0
|
CA
|
B:GLY270
|
4.6
|
15.0
|
1.0
|
HB3
|
B:HIS116
|
4.6
|
19.5
|
1.0
|
HE1
|
B:HIS116
|
4.6
|
20.0
|
1.0
|
HA
|
B:THR118
|
4.7
|
17.6
|
1.0
|
HG2
|
B:GLU268
|
4.7
|
18.9
|
1.0
|
CE1
|
B:HIS116
|
4.7
|
16.7
|
1.0
|
HB2
|
B:SER65
|
4.7
|
19.5
|
0.5
|
ZN
|
B:ZN1103
|
4.7
|
16.4
|
1.0
|
HB1
|
B:ALA117
|
4.7
|
19.5
|
1.0
|
HD3
|
B:PRO119
|
4.8
|
19.0
|
1.0
|
OD2
|
B:ASP315
|
4.8
|
15.8
|
1.0
|
OG1
|
B:THR112
|
4.9
|
16.6
|
1.0
|
HG1
|
B:THR112
|
4.9
|
19.9
|
1.0
|
HG21
|
B:THR118
|
4.9
|
19.0
|
1.0
|
H
|
B:ALA117
|
5.0
|
18.7
|
1.0
|
|
Magnesium binding site 4 out
of 4 in 7qow
Go back to
Magnesium Binding Sites List in 7qow
Magnesium binding site 4 out
of 4 in the Crystal Structure of Vibrio Alkaline Phosphatase in 1.0 M Nacl
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 4 of Crystal Structure of Vibrio Alkaline Phosphatase in 1.0 M Nacl within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg1110
b:17.4
occ:1.00
|
O
|
A:SER485
|
2.2
|
16.0
|
1.0
|
O
|
B:GLY48
|
2.3
|
15.7
|
1.0
|
O
|
A:HOH1019
|
2.4
|
23.8
|
1.0
|
O
|
B:ALA45
|
2.4
|
17.7
|
1.0
|
O
|
B:GLN46
|
2.4
|
16.2
|
1.0
|
C
|
B:GLN46
|
3.1
|
15.9
|
1.0
|
HB3
|
A:LYS486
|
3.1
|
19.3
|
1.0
|
HA
|
B:GLN46
|
3.2
|
19.1
|
1.0
|
C
|
B:GLY48
|
3.2
|
15.6
|
1.0
|
C
|
A:SER485
|
3.4
|
15.3
|
1.0
|
HA
|
B:VAL49
|
3.5
|
17.6
|
1.0
|
C
|
B:ALA45
|
3.5
|
16.1
|
1.0
|
CA
|
B:GLN46
|
3.6
|
16.0
|
1.0
|
O
|
B:HOH1243
|
3.6
|
28.5
|
1.0
|
HA
|
A:LYS486
|
3.7
|
17.6
|
1.0
|
O
|
A:HOH1054
|
3.7
|
34.8
|
1.0
|
N
|
B:GLY48
|
3.8
|
15.8
|
1.0
|
H
|
B:GLY48
|
3.8
|
18.9
|
1.0
|
O
|
B:HOH1442
|
3.8
|
21.8
|
1.0
|
HB3
|
A:SER485
|
3.8
|
18.6
|
1.0
|
CB
|
A:LYS486
|
3.9
|
16.1
|
1.0
|
N
|
B:GLN46
|
4.0
|
15.7
|
1.0
|
N
|
B:GLU47
|
4.0
|
16.4
|
1.0
|
C
|
B:GLU47
|
4.1
|
16.3
|
1.0
|
N
|
B:VAL49
|
4.1
|
15.0
|
1.0
|
CA
|
A:LYS486
|
4.1
|
14.7
|
1.0
|
CA
|
B:GLY48
|
4.1
|
15.4
|
1.0
|
N
|
A:LYS486
|
4.2
|
15.1
|
1.0
|
HB2
|
A:LYS486
|
4.2
|
19.3
|
1.0
|
CA
|
B:VAL49
|
4.2
|
14.7
|
1.0
|
HG12
|
B:VAL49
|
4.4
|
18.9
|
1.0
|
CA
|
A:SER485
|
4.4
|
15.2
|
1.0
|
CB
|
A:SER485
|
4.5
|
15.5
|
1.0
|
CA
|
B:GLU47
|
4.5
|
16.9
|
1.0
|
O
|
B:GLU47
|
4.6
|
19.1
|
1.0
|
HA
|
B:GLU47
|
4.6
|
20.3
|
1.0
|
H
|
B:GLU47
|
4.7
|
19.7
|
1.0
|
HA2
|
B:GLY48
|
4.7
|
18.4
|
1.0
|
HA
|
B:ALA45
|
4.7
|
19.4
|
1.0
|
HA3
|
B:GLY48
|
4.8
|
18.4
|
1.0
|
O
|
A:LEU482
|
4.8
|
16.8
|
1.0
|
CA
|
B:ALA45
|
4.8
|
16.2
|
1.0
|
H
|
A:SER485
|
4.8
|
18.5
|
1.0
|
H
|
B:VAL49
|
4.9
|
18.0
|
1.0
|
H
|
B:GLN46
|
4.9
|
18.8
|
1.0
|
OG
|
A:SER485
|
4.9
|
15.2
|
1.0
|
HG2
|
B:GLN46
|
4.9
|
24.3
|
1.0
|
CB
|
B:GLN46
|
5.0
|
17.5
|
1.0
|
N
|
A:SER485
|
5.0
|
15.4
|
1.0
|
HG13
|
B:ILE50
|
5.0
|
18.2
|
1.0
|
H
|
A:LYS486
|
5.0
|
18.0
|
1.0
|
|
Reference:
S.Markusson,
J.G.Hjorleifsson,
P.Kursula,
B.Asgeirsson.
Structural Characterization of Functionally Important Chloride Binding Sites in the Marine Vibrio Alkaline Phosphatase. Biochemistry V. 61 2248 2022.
ISSN: ISSN 0006-2960
PubMed: 36194497
DOI: 10.1021/ACS.BIOCHEM.2C00438
Page generated: Thu Oct 3 05:15:44 2024
|