Magnesium in PDB 2ofw: Crystal Structure of the Apsk Domain of Human PAPSS1 Complexed with 2 Aps Molecules
Enzymatic activity of Crystal Structure of the Apsk Domain of Human PAPSS1 Complexed with 2 Aps Molecules
All present enzymatic activity of Crystal Structure of the Apsk Domain of Human PAPSS1 Complexed with 2 Aps Molecules:
2.7.1.25;
Protein crystallography data
The structure of Crystal Structure of the Apsk Domain of Human PAPSS1 Complexed with 2 Aps Molecules, PDB code: 2ofw
was solved by
N.Sekulic,
A.Lavie,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
10.00 /
2.05
|
Space group
|
C 1 2 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
181.190,
69.030,
150.610,
90.00,
116.61,
90.00
|
R / Rfree (%)
|
21.7 /
28.2
|
Magnesium Binding Sites:
The binding sites of Magnesium atom in the Crystal Structure of the Apsk Domain of Human PAPSS1 Complexed with 2 Aps Molecules
(pdb code 2ofw). This binding sites where shown within
5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the
Crystal Structure of the Apsk Domain of Human PAPSS1 Complexed with 2 Aps Molecules, PDB code: 2ofw:
Jump to Magnesium binding site number:
1;
2;
3;
4;
5;
6;
Magnesium binding site 1 out
of 6 in 2ofw
Go back to
Magnesium Binding Sites List in 2ofw
Magnesium binding site 1 out
of 6 in the Crystal Structure of the Apsk Domain of Human PAPSS1 Complexed with 2 Aps Molecules
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 the Apsk Domain of Human PAPSS1 Complexed with 2 Aps Molecules within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg1002
b:18.2
occ:1.00
|
O
|
B:HOH1290
|
1.8
|
24.9
|
1.0
|
O
|
B:HOH1204
|
2.2
|
25.8
|
1.0
|
O
|
B:HOH1203
|
2.3
|
21.4
|
1.0
|
OG1
|
B:THR66
|
2.3
|
22.1
|
1.0
|
O
|
B:HOH1202
|
2.3
|
27.9
|
1.0
|
O2B
|
B:ADX1201
|
2.3
|
22.0
|
1.0
|
SB
|
B:ADX1201
|
3.4
|
23.2
|
1.0
|
O3B
|
B:ADX1201
|
3.4
|
21.2
|
1.0
|
O
|
B:HOH1205
|
3.6
|
25.4
|
1.0
|
O
|
B:HOH1276
|
3.6
|
27.1
|
1.0
|
CB
|
B:THR66
|
3.7
|
21.1
|
1.0
|
O
|
B:HOH1261
|
3.8
|
32.3
|
1.0
|
OD2
|
B:ASP87
|
4.0
|
26.5
|
1.0
|
O2A
|
B:ADX1201
|
4.1
|
24.4
|
1.0
|
N
|
B:THR66
|
4.3
|
19.9
|
1.0
|
OE1
|
A:GLN31
|
4.3
|
46.9
|
1.0
|
O3'
|
B:ADX1200
|
4.3
|
25.9
|
1.0
|
O1B
|
B:ADX1201
|
4.3
|
24.0
|
1.0
|
OD1
|
B:ASP87
|
4.4
|
25.2
|
1.0
|
O
|
B:HOH1243
|
4.5
|
36.6
|
1.0
|
CA
|
B:THR66
|
4.5
|
21.7
|
1.0
|
NZ
|
B:LYS171
|
4.5
|
30.0
|
1.0
|
CD
|
A:GLN31
|
4.5
|
44.0
|
1.0
|
O3A
|
B:ADX1201
|
4.6
|
22.2
|
1.0
|
CG2
|
B:THR66
|
4.6
|
21.6
|
1.0
|
CG
|
B:ASP87
|
4.6
|
24.4
|
1.0
|
CE
|
B:LYS65
|
4.6
|
18.0
|
1.0
|
O
|
B:HOH1283
|
4.8
|
26.7
|
1.0
|
PA
|
B:ADX1201
|
4.8
|
23.6
|
1.0
|
CG
|
A:GLN31
|
4.9
|
43.9
|
1.0
|
NZ
|
B:LYS65
|
4.9
|
16.8
|
1.0
|
NE2
|
A:GLN31
|
4.9
|
42.9
|
1.0
|
CB
|
B:LYS65
|
4.9
|
19.3
|
1.0
|
|
Magnesium binding site 2 out
of 6 in 2ofw
Go back to
Magnesium Binding Sites List in 2ofw
Magnesium binding site 2 out
of 6 in the Crystal Structure of the Apsk Domain of Human PAPSS1 Complexed with 2 Aps Molecules
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 the Apsk Domain of Human PAPSS1 Complexed with 2 Aps Molecules within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Mg1003
b:18.2
occ:1.00
|
O
|
C:HOH1304
|
2.1
|
20.3
|
1.0
|
O
|
C:HOH1303
|
2.1
|
23.2
|
1.0
|
O
|
C:HOH1302
|
2.2
|
28.8
|
1.0
|
OG1
|
C:THR66
|
2.2
|
20.5
|
1.0
|
O
|
D:HOH1402
|
2.3
|
21.9
|
1.0
|
O2B
|
C:ADX1301
|
2.4
|
19.8
|
1.0
|
CB
|
C:THR66
|
3.5
|
20.7
|
1.0
|
SB
|
C:ADX1301
|
3.5
|
18.6
|
1.0
|
O3B
|
C:ADX1301
|
3.5
|
13.7
|
1.0
|
OD2
|
C:ASP89
|
3.7
|
25.1
|
1.0
|
O
|
C:HOH1374
|
3.9
|
21.9
|
1.0
|
OD1
|
C:ASP87
|
4.0
|
22.9
|
1.0
|
O2A
|
C:ADX1301
|
4.2
|
21.0
|
1.0
|
NE2
|
D:GLN31
|
4.2
|
35.6
|
1.0
|
OD2
|
C:ASP87
|
4.3
|
20.5
|
1.0
|
O
|
C:HOH1333
|
4.3
|
31.9
|
1.0
|
N
|
C:THR66
|
4.3
|
20.1
|
1.0
|
CG2
|
C:THR66
|
4.4
|
21.9
|
1.0
|
O3'
|
C:ADX1300
|
4.5
|
26.4
|
1.0
|
CA
|
C:THR66
|
4.5
|
20.9
|
1.0
|
O1B
|
C:ADX1301
|
4.5
|
18.1
|
1.0
|
O3A
|
C:ADX1301
|
4.6
|
18.2
|
1.0
|
CG
|
C:ASP87
|
4.6
|
21.2
|
1.0
|
PA
|
C:ADX1301
|
4.8
|
22.2
|
1.0
|
CG
|
C:ASP89
|
4.8
|
21.1
|
1.0
|
CG
|
D:GLN31
|
4.8
|
35.5
|
1.0
|
NZ
|
C:LYS171
|
5.0
|
33.4
|
1.0
|
O
|
C:SER130
|
5.0
|
17.5
|
1.0
|
|
Magnesium binding site 3 out
of 6 in 2ofw
Go back to
Magnesium Binding Sites List in 2ofw
Magnesium binding site 3 out
of 6 in the Crystal Structure of the Apsk Domain of Human PAPSS1 Complexed with 2 Aps Molecules
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 the Apsk Domain of Human PAPSS1 Complexed with 2 Aps Molecules within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Mg1004
b:15.2
occ:1.00
|
O
|
D:HOH1406
|
1.7
|
23.1
|
1.0
|
OG1
|
D:THR66
|
2.0
|
21.0
|
1.0
|
O
|
D:HOH1404
|
2.1
|
25.2
|
1.0
|
O
|
D:HOH1403
|
2.1
|
16.8
|
1.0
|
O
|
D:HOH1405
|
2.1
|
12.3
|
1.0
|
O2B
|
D:ADX1401
|
2.2
|
25.0
|
1.0
|
CB
|
D:THR66
|
3.2
|
21.9
|
1.0
|
SB
|
D:ADX1401
|
3.4
|
22.2
|
1.0
|
O3B
|
D:ADX1401
|
3.5
|
23.9
|
1.0
|
OD1
|
D:ASP87
|
3.9
|
20.5
|
1.0
|
OD1
|
D:ASP89
|
4.0
|
22.8
|
1.0
|
N
|
D:THR66
|
4.0
|
21.0
|
1.0
|
OD2
|
D:ASP87
|
4.1
|
17.7
|
1.0
|
O
|
D:HOH1442
|
4.1
|
27.7
|
1.0
|
O
|
D:HOH1430
|
4.1
|
23.9
|
1.0
|
CG2
|
D:THR66
|
4.1
|
21.0
|
1.0
|
CA
|
D:THR66
|
4.2
|
21.1
|
1.0
|
O2A
|
D:ADX1401
|
4.2
|
25.1
|
1.0
|
O1B
|
D:ADX1401
|
4.4
|
21.6
|
1.0
|
O3A
|
D:ADX1401
|
4.4
|
25.5
|
1.0
|
CG
|
D:ASP87
|
4.4
|
17.6
|
1.0
|
NE2
|
C:GLN31
|
4.5
|
29.0
|
1.0
|
PA
|
D:ADX1401
|
4.7
|
27.6
|
1.0
|
CG
|
C:GLN31
|
4.7
|
25.6
|
1.0
|
O3'
|
D:ADX1400
|
4.7
|
22.4
|
1.0
|
O
|
D:HOH1483
|
4.7
|
30.0
|
1.0
|
CD
|
C:GLN31
|
4.9
|
27.7
|
1.0
|
CG
|
D:ASP89
|
5.0
|
19.8
|
1.0
|
O1A
|
D:ADX1401
|
5.0
|
26.7
|
1.0
|
CE
|
D:LYS65
|
5.0
|
17.0
|
1.0
|
|
Magnesium binding site 4 out
of 6 in 2ofw
Go back to
Magnesium Binding Sites List in 2ofw
Magnesium binding site 4 out
of 6 in the Crystal Structure of the Apsk Domain of Human PAPSS1 Complexed with 2 Aps Molecules
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 the Apsk Domain of Human PAPSS1 Complexed with 2 Aps Molecules within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Mg1005
b:27.6
occ:1.00
|
O
|
E:HOH1502
|
2.2
|
19.8
|
1.0
|
OG1
|
E:THR66
|
2.3
|
25.6
|
1.0
|
O2B
|
E:ADX1501
|
2.3
|
20.2
|
1.0
|
O
|
E:HOH1503
|
2.3
|
27.8
|
1.0
|
O
|
E:HOH1504
|
2.6
|
31.4
|
1.0
|
O3B
|
E:ADX1501
|
3.1
|
20.7
|
1.0
|
SB
|
E:ADX1501
|
3.3
|
23.4
|
1.0
|
CB
|
E:THR66
|
3.5
|
25.1
|
1.0
|
OD2
|
E:ASP89
|
3.7
|
24.0
|
1.0
|
O
|
E:HOH1521
|
4.0
|
21.8
|
1.0
|
O
|
E:HOH1534
|
4.0
|
23.4
|
1.0
|
O2A
|
E:ADX1501
|
4.1
|
24.0
|
1.0
|
OD1
|
E:ASP87
|
4.1
|
25.8
|
1.0
|
N
|
E:THR66
|
4.3
|
23.7
|
1.0
|
O1B
|
E:ADX1501
|
4.3
|
25.0
|
1.0
|
OD2
|
E:ASP87
|
4.3
|
23.3
|
1.0
|
O3A
|
E:ADX1501
|
4.4
|
23.8
|
1.0
|
O3'
|
E:ADX1500
|
4.4
|
22.1
|
1.0
|
CG2
|
E:THR66
|
4.5
|
26.3
|
1.0
|
CA
|
E:THR66
|
4.5
|
25.2
|
1.0
|
PA
|
E:ADX1501
|
4.7
|
25.4
|
1.0
|
O
|
E:HOH1582
|
4.7
|
25.5
|
1.0
|
CG
|
E:ASP87
|
4.7
|
24.2
|
1.0
|
NE2
|
F:GLN31
|
4.7
|
35.6
|
1.0
|
CG
|
E:ASP89
|
4.8
|
24.6
|
1.0
|
CG
|
F:GLN31
|
4.9
|
37.4
|
1.0
|
NZ
|
E:LYS65
|
4.9
|
23.9
|
1.0
|
CE
|
E:LYS65
|
5.0
|
21.5
|
1.0
|
|
Magnesium binding site 5 out
of 6 in 2ofw
Go back to
Magnesium Binding Sites List in 2ofw
Magnesium binding site 5 out
of 6 in the Crystal Structure of the Apsk Domain of Human PAPSS1 Complexed with 2 Aps Molecules
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 5 of Crystal Structure of the Apsk Domain of Human PAPSS1 Complexed with 2 Aps Molecules within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:Mg1006
b:19.3
occ:1.00
|
O
|
F:HOH1605
|
1.9
|
17.0
|
1.0
|
OG1
|
F:THR66
|
2.1
|
20.8
|
1.0
|
O
|
F:HOH1602
|
2.1
|
22.5
|
1.0
|
O2B
|
F:ADX1601
|
2.2
|
21.0
|
1.0
|
O
|
F:HOH1603
|
2.4
|
20.0
|
1.0
|
O
|
F:HOH1604
|
2.5
|
24.1
|
1.0
|
SB
|
F:ADX1601
|
3.3
|
20.9
|
1.0
|
CB
|
F:THR66
|
3.3
|
20.2
|
1.0
|
O3B
|
F:ADX1601
|
3.4
|
19.2
|
1.0
|
OD2
|
F:ASP89
|
3.9
|
20.1
|
1.0
|
OD1
|
F:ASP87
|
3.9
|
21.0
|
1.0
|
O2A
|
F:ADX1601
|
4.0
|
21.9
|
1.0
|
O
|
F:HOH1669
|
4.1
|
26.9
|
1.0
|
O
|
F:HOH1607
|
4.2
|
26.9
|
1.0
|
N
|
F:THR66
|
4.2
|
20.3
|
1.0
|
OD2
|
F:ASP87
|
4.3
|
19.1
|
1.0
|
CG2
|
F:THR66
|
4.3
|
20.8
|
1.0
|
CA
|
F:THR66
|
4.3
|
20.1
|
1.0
|
O3A
|
F:ADX1601
|
4.3
|
21.7
|
1.0
|
O1B
|
F:ADX1601
|
4.3
|
22.4
|
1.0
|
PA
|
F:ADX1601
|
4.5
|
20.8
|
1.0
|
CG
|
F:ASP87
|
4.5
|
19.1
|
1.0
|
O3'
|
F:ADX1600
|
4.5
|
22.1
|
1.0
|
CG
|
E:GLN31
|
4.7
|
29.5
|
1.0
|
NE2
|
E:GLN31
|
4.8
|
29.7
|
1.0
|
O1A
|
F:ADX1601
|
4.8
|
22.2
|
1.0
|
O
|
F:HOH1634
|
4.8
|
22.7
|
1.0
|
CG
|
F:ASP89
|
4.9
|
20.5
|
1.0
|
CD
|
E:GLN31
|
5.0
|
29.9
|
1.0
|
CE
|
F:LYS65
|
5.0
|
23.9
|
1.0
|
|
Magnesium binding site 6 out
of 6 in 2ofw
Go back to
Magnesium Binding Sites List in 2ofw
Magnesium binding site 6 out
of 6 in the Crystal Structure of the Apsk Domain of Human PAPSS1 Complexed with 2 Aps Molecules
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 6 of Crystal Structure of the Apsk Domain of Human PAPSS1 Complexed with 2 Aps Molecules within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
H:Mg1008
b:20.1
occ:1.00
|
O2B
|
H:ADX1801
|
2.1
|
25.8
|
1.0
|
O
|
H:HOH1805
|
2.1
|
23.8
|
1.0
|
O
|
H:HOH1803
|
2.2
|
24.7
|
1.0
|
O
|
H:HOH1802
|
2.2
|
23.4
|
1.0
|
OG1
|
H:THR66
|
2.2
|
26.6
|
1.0
|
O
|
H:HOH1903
|
2.4
|
41.7
|
1.0
|
SB
|
H:ADX1801
|
3.3
|
24.4
|
1.0
|
CB
|
H:THR66
|
3.4
|
25.6
|
1.0
|
O
|
H:HOH1804
|
3.5
|
40.8
|
1.0
|
O3B
|
H:ADX1801
|
3.5
|
21.3
|
1.0
|
OD1
|
H:ASP87
|
3.9
|
24.9
|
1.0
|
O2A
|
H:ADX1801
|
3.9
|
27.5
|
1.0
|
OD1
|
H:ASP89
|
4.1
|
27.5
|
1.0
|
N
|
H:THR66
|
4.1
|
24.5
|
1.0
|
O
|
H:HOH1835
|
4.2
|
35.4
|
1.0
|
O1B
|
H:ADX1801
|
4.3
|
22.8
|
1.0
|
CA
|
H:THR66
|
4.3
|
25.7
|
1.0
|
OD2
|
H:ASP87
|
4.3
|
26.8
|
1.0
|
O3A
|
H:ADX1801
|
4.4
|
25.1
|
1.0
|
CG2
|
H:THR66
|
4.4
|
25.7
|
1.0
|
NE2
|
G:GLN31
|
4.5
|
38.4
|
1.0
|
PA
|
H:ADX1801
|
4.6
|
28.8
|
1.0
|
CG
|
H:ASP87
|
4.6
|
24.1
|
1.0
|
O3'
|
H:ADX1800
|
4.7
|
22.6
|
1.0
|
CG
|
G:GLN31
|
4.9
|
37.9
|
1.0
|
CE
|
H:LYS65
|
4.9
|
18.1
|
1.0
|
O
|
H:HOH1840
|
5.0
|
38.5
|
1.0
|
CD
|
G:GLN31
|
5.0
|
37.9
|
1.0
|
|
Reference:
N.Sekulic,
K.Dietrich,
I.Paarmann,
S.Ort,
M.Konrad,
A.Lavie.
Elucidation of the Active Conformation of the Aps-Kinase Domain of Human Paps Synthetase 1. J.Mol.Biol. V. 367 488 2007.
ISSN: ISSN 0022-2836
PubMed: 17276460
DOI: 10.1016/J.JMB.2007.01.025
Page generated: Wed Aug 14 01:26:59 2024
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