Magnesium in PDB 1q9w: S45-18 Fab Pentasaccharide Bisphosphate Complex
Protein crystallography data
The structure of S45-18 Fab Pentasaccharide Bisphosphate Complex, PDB code: 1q9w
was solved by
H.P.Nguyen,
N.O.Seto,
C.R.Mackenzie,
L.Brade,
P.Kosma,
H.Brade,
S.V.Evans,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
19.90 /
1.75
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
71.200,
113.900,
133.900,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
21.2 /
24.7
|
Magnesium Binding Sites:
The binding sites of Magnesium atom in the S45-18 Fab Pentasaccharide Bisphosphate Complex
(pdb code 1q9w). This binding sites where shown within
5.0 Angstroms radius around Magnesium atom.
In total 5 binding sites of Magnesium where determined in the
S45-18 Fab Pentasaccharide Bisphosphate Complex, PDB code: 1q9w:
Jump to Magnesium binding site number:
1;
2;
3;
4;
5;
Magnesium binding site 1 out
of 5 in 1q9w
Go back to
Magnesium Binding Sites List in 1q9w
Magnesium binding site 1 out
of 5 in the S45-18 Fab Pentasaccharide Bisphosphate Complex
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 1 of S45-18 Fab Pentasaccharide Bisphosphate Complex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg214
b:16.9
occ:1.00
|
O
|
B:HOH312
|
2.9
|
20.2
|
1.0
|
N
|
A:PHE97
|
3.1
|
16.8
|
1.0
|
N
|
B:TRP47
|
3.2
|
17.2
|
1.0
|
O
|
B:HOH431
|
3.5
|
33.0
|
1.0
|
CA
|
B:GLU46
|
3.6
|
17.5
|
1.0
|
CA
|
A:THR96
|
3.7
|
16.2
|
1.0
|
CG2
|
A:THR96
|
3.9
|
20.4
|
1.0
|
CD2
|
A:PHE97
|
3.9
|
17.8
|
1.0
|
C
|
B:GLU46
|
3.9
|
18.2
|
1.0
|
C
|
A:THR96
|
3.9
|
16.0
|
1.0
|
CB
|
A:PHE97
|
3.9
|
17.7
|
1.0
|
O
|
B:HOH434
|
4.0
|
31.6
|
1.0
|
CA
|
A:PHE97
|
4.0
|
17.9
|
1.0
|
CG
|
B:GLU46
|
4.1
|
18.2
|
1.0
|
O
|
B:LEU45
|
4.1
|
17.6
|
1.0
|
CB
|
B:TRP47
|
4.1
|
18.0
|
1.0
|
O
|
A:PHE97
|
4.2
|
16.8
|
1.0
|
CA
|
B:TRP47
|
4.2
|
18.6
|
1.0
|
O
|
B:HOH322
|
4.3
|
22.2
|
1.0
|
CB
|
B:GLU46
|
4.3
|
16.7
|
1.0
|
CG
|
A:PHE97
|
4.4
|
15.9
|
1.0
|
CB
|
A:THR96
|
4.4
|
18.7
|
1.0
|
O
|
B:TRP47
|
4.4
|
18.1
|
1.0
|
O
|
A:HOH255
|
4.5
|
25.6
|
1.0
|
O
|
A:ARG95
|
4.6
|
16.3
|
1.0
|
C
|
A:PHE97
|
4.6
|
17.2
|
1.0
|
N
|
B:GLU46
|
4.6
|
14.7
|
1.0
|
N
|
A:THR96
|
4.8
|
15.5
|
1.0
|
C
|
B:LEU45
|
4.8
|
17.4
|
1.0
|
C
|
B:TRP47
|
4.8
|
17.9
|
1.0
|
CE2
|
A:PHE97
|
5.0
|
16.6
|
1.0
|
|
Magnesium binding site 2 out
of 5 in 1q9w
Go back to
Magnesium Binding Sites List in 1q9w
Magnesium binding site 2 out
of 5 in the S45-18 Fab Pentasaccharide Bisphosphate Complex
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 2 of S45-18 Fab Pentasaccharide Bisphosphate Complex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg215
b:26.0
occ:1.00
|
OG1
|
A:THR101
|
2.8
|
17.3
|
1.0
|
O
|
A:SER22
|
2.8
|
19.0
|
1.0
|
NE2
|
A:GLN6
|
2.9
|
14.6
|
1.0
|
CB
|
A:GLN6
|
3.4
|
17.9
|
1.0
|
CB
|
A:MET21
|
3.4
|
21.6
|
1.0
|
CG
|
A:MET21
|
3.5
|
20.7
|
1.0
|
N
|
A:SER22
|
3.6
|
15.9
|
1.0
|
CB
|
A:THR101
|
3.6
|
16.7
|
1.0
|
C
|
A:SER22
|
3.6
|
15.9
|
1.0
|
CG
|
A:GLN6
|
3.6
|
16.3
|
1.0
|
CZ3
|
A:TRP35
|
3.7
|
20.9
|
1.0
|
CH2
|
A:TRP35
|
3.7
|
19.9
|
1.0
|
CD
|
A:GLN6
|
3.7
|
15.4
|
1.0
|
SD
|
A:MET21
|
3.8
|
24.4
|
1.0
|
C
|
A:MET21
|
3.9
|
21.1
|
1.0
|
CA
|
A:SER22
|
4.1
|
16.8
|
1.0
|
N
|
A:PHE7
|
4.2
|
15.8
|
1.0
|
CA
|
A:MET21
|
4.2
|
20.9
|
1.0
|
O
|
A:PHE7
|
4.3
|
17.6
|
1.0
|
CA
|
A:GLN6
|
4.3
|
16.8
|
1.0
|
CG2
|
A:THR101
|
4.5
|
17.3
|
1.0
|
O
|
A:MET21
|
4.5
|
21.1
|
1.0
|
N
|
A:CYS23
|
4.6
|
17.0
|
1.0
|
C
|
A:GLN6
|
4.7
|
18.2
|
1.0
|
CA
|
A:THR101
|
4.7
|
16.5
|
1.0
|
N
|
A:THR101
|
4.7
|
17.6
|
1.0
|
C
|
A:PHE7
|
4.8
|
16.5
|
1.0
|
O
|
A:TYR86
|
4.8
|
19.1
|
1.0
|
OE1
|
A:GLN6
|
4.9
|
18.7
|
1.0
|
CE3
|
A:TRP35
|
5.0
|
19.0
|
1.0
|
CA
|
A:CYS23
|
5.0
|
16.9
|
1.0
|
|
Magnesium binding site 3 out
of 5 in 1q9w
Go back to
Magnesium Binding Sites List in 1q9w
Magnesium binding site 3 out
of 5 in the S45-18 Fab Pentasaccharide Bisphosphate Complex
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 3 of S45-18 Fab Pentasaccharide Bisphosphate Complex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg306
b:23.1
occ:1.00
|
O
|
B:HOH379
|
2.0
|
24.3
|
1.0
|
O
|
B:HOH376
|
2.0
|
24.2
|
1.0
|
O
|
B:HOH378
|
2.1
|
25.0
|
1.0
|
O
|
B:HOH377
|
2.1
|
22.3
|
1.0
|
OE2
|
B:GLU56
|
2.1
|
22.1
|
1.0
|
CD
|
B:GLU56
|
3.2
|
24.1
|
1.0
|
OE1
|
B:GLU56
|
3.5
|
22.6
|
1.0
|
O
|
B:THR55
|
4.0
|
19.7
|
1.0
|
NH1
|
B:ARG52
|
4.2
|
20.7
|
1.0
|
O
|
B:HOH490
|
4.3
|
33.6
|
1.0
|
CG
|
B:GLU56
|
4.4
|
20.2
|
1.0
|
CB
|
B:THR54
|
4.7
|
19.9
|
1.0
|
|
Magnesium binding site 4 out
of 5 in 1q9w
Go back to
Magnesium Binding Sites List in 1q9w
Magnesium binding site 4 out
of 5 in the S45-18 Fab Pentasaccharide Bisphosphate Complex
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 4 of S45-18 Fab Pentasaccharide Bisphosphate Complex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Mg314
b:24.7
occ:1.00
|
O
|
C:HOH397
|
2.7
|
38.4
|
1.0
|
O
|
D:HOH344
|
2.7
|
32.8
|
1.0
|
N
|
C:PHE97
|
3.1
|
22.3
|
1.0
|
N
|
D:TRP47
|
3.1
|
18.5
|
1.0
|
CA
|
D:GLU46
|
3.6
|
18.2
|
1.0
|
CA
|
C:THR96
|
3.7
|
23.5
|
1.0
|
C
|
C:THR96
|
3.9
|
22.7
|
1.0
|
C
|
D:GLU46
|
3.9
|
19.9
|
1.0
|
CG2
|
C:THR96
|
3.9
|
27.0
|
1.0
|
CD2
|
C:PHE97
|
4.0
|
20.5
|
1.0
|
CB
|
D:TRP47
|
4.0
|
20.3
|
1.0
|
CB
|
C:PHE97
|
4.0
|
22.2
|
1.0
|
CA
|
C:PHE97
|
4.0
|
21.6
|
1.0
|
CG
|
D:GLU46
|
4.1
|
22.2
|
1.0
|
O
|
C:PHE97
|
4.1
|
22.3
|
1.0
|
CA
|
D:TRP47
|
4.1
|
19.5
|
1.0
|
O
|
D:HOH384
|
4.2
|
36.1
|
1.0
|
O
|
D:LEU45
|
4.2
|
19.1
|
1.0
|
O
|
C:HOH443
|
4.2
|
35.5
|
1.0
|
CB
|
D:GLU46
|
4.4
|
19.8
|
1.0
|
CB
|
C:THR96
|
4.4
|
23.9
|
1.0
|
O
|
D:TRP47
|
4.4
|
21.9
|
1.0
|
CG
|
C:PHE97
|
4.5
|
19.8
|
1.0
|
O
|
C:ARG95
|
4.5
|
22.0
|
1.0
|
C
|
C:PHE97
|
4.6
|
21.9
|
1.0
|
N
|
D:GLU46
|
4.7
|
19.4
|
1.0
|
N
|
C:THR96
|
4.7
|
23.3
|
1.0
|
C
|
D:TRP47
|
4.8
|
21.2
|
1.0
|
C
|
D:LEU45
|
4.9
|
20.1
|
1.0
|
|
Magnesium binding site 5 out
of 5 in 1q9w
Go back to
Magnesium Binding Sites List in 1q9w
Magnesium binding site 5 out
of 5 in the S45-18 Fab Pentasaccharide Bisphosphate Complex
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 5 of S45-18 Fab Pentasaccharide Bisphosphate Complex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Mg315
b:32.5
occ:1.00
|
OG1
|
C:THR101
|
2.7
|
21.2
|
1.0
|
NE2
|
C:GLN6
|
2.9
|
21.2
|
1.0
|
O
|
C:SER22
|
2.9
|
24.2
|
1.0
|
CB
|
C:MET21
|
3.5
|
24.4
|
1.0
|
CB
|
C:GLN6
|
3.5
|
25.6
|
1.0
|
CG
|
C:MET21
|
3.6
|
24.7
|
1.0
|
CB
|
C:THR101
|
3.6
|
22.4
|
1.0
|
CG
|
C:GLN6
|
3.7
|
24.2
|
1.0
|
C
|
C:SER22
|
3.7
|
25.9
|
1.0
|
N
|
C:SER22
|
3.7
|
24.5
|
1.0
|
CD
|
C:GLN6
|
3.7
|
24.2
|
1.0
|
CZ3
|
C:TRP35
|
3.8
|
24.3
|
1.0
|
CH2
|
C:TRP35
|
3.9
|
23.4
|
1.0
|
SD
|
C:MET21
|
3.9
|
27.1
|
1.0
|
C
|
C:MET21
|
4.0
|
25.0
|
1.0
|
O
|
C:PHE7
|
4.0
|
25.6
|
1.0
|
N
|
C:PHE7
|
4.1
|
25.9
|
1.0
|
CA
|
C:SER22
|
4.3
|
26.7
|
1.0
|
CA
|
C:GLN6
|
4.3
|
26.9
|
1.0
|
CA
|
C:MET21
|
4.3
|
25.7
|
1.0
|
O
|
C:MET21
|
4.5
|
24.0
|
1.0
|
CG2
|
C:THR101
|
4.5
|
22.7
|
1.0
|
C
|
C:PHE7
|
4.6
|
25.7
|
1.0
|
C
|
C:GLN6
|
4.6
|
26.8
|
1.0
|
N
|
C:CYS23
|
4.6
|
25.7
|
1.0
|
CA
|
C:THR101
|
4.8
|
22.0
|
1.0
|
N
|
C:THR101
|
4.8
|
22.8
|
1.0
|
O
|
C:TYR86
|
4.8
|
20.7
|
1.0
|
CB
|
C:CYS23
|
4.9
|
26.5
|
1.0
|
OE1
|
C:GLN6
|
4.9
|
23.4
|
1.0
|
CA
|
C:CYS23
|
4.9
|
26.7
|
1.0
|
O
|
C:PRO8
|
5.0
|
24.0
|
1.0
|
CA
|
C:PHE7
|
5.0
|
26.9
|
1.0
|
|
Reference:
H.P.Nguyen,
N.O.Seto,
C.R.Mackenzie,
L.Brade,
P.Kosma,
H.Brade,
S.V.Evans.
Germline Antibody Recognition of Distinct Carbohydrate Epitopes. Nat.Struct.Biol. V. 10 1019 2003.
ISSN: ISSN 1072-8368
PubMed: 14625588
DOI: 10.1038/NSB1014
Page generated: Tue Aug 13 11:13:52 2024
|