Magnesium in PDB 1q9l: S25-2 Fab Unliganded 2
Protein crystallography data
The structure of S25-2 Fab Unliganded 2, PDB code: 1q9l
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)
|
19.85 /
2.28
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
84.700,
96.000,
114.200,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
21.6 /
28.6
|
Other elements in 1q9l:
The structure of S25-2 Fab Unliganded 2 also contains other interesting chemical elements:
Magnesium Binding Sites:
The binding sites of Magnesium atom in the S25-2 Fab Unliganded 2
(pdb code 1q9l). This binding sites where shown within
5.0 Angstroms radius around Magnesium atom.
In total 7 binding sites of Magnesium where determined in the
S25-2 Fab Unliganded 2, PDB code: 1q9l:
Jump to Magnesium binding site number:
1;
2;
3;
4;
5;
6;
7;
Magnesium binding site 1 out
of 7 in 1q9l
Go back to
Magnesium Binding Sites List in 1q9l
Magnesium binding site 1 out
of 7 in the S25-2 Fab Unliganded 2
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 1 of S25-2 Fab Unliganded 2 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg212
b:27.1
occ:1.00
|
O
|
B:HOH362
|
2.8
|
26.9
|
1.0
|
N
|
A:PHE97
|
3.1
|
26.8
|
1.0
|
N
|
B:TRP47
|
3.3
|
28.7
|
1.0
|
O
|
B:HOH341
|
3.6
|
39.1
|
1.0
|
CA
|
A:THR96
|
3.6
|
27.2
|
1.0
|
CA
|
B:GLU46
|
3.8
|
29.2
|
1.0
|
C
|
A:THR96
|
3.9
|
27.0
|
1.0
|
CD2
|
A:PHE97
|
3.9
|
27.9
|
1.0
|
OG1
|
A:THR96
|
3.9
|
30.3
|
1.0
|
CB
|
A:THR96
|
3.9
|
26.4
|
1.0
|
CB
|
B:TRP47
|
4.0
|
27.8
|
1.0
|
CB
|
A:PHE97
|
4.0
|
25.4
|
1.0
|
CA
|
A:PHE97
|
4.0
|
27.6
|
1.0
|
C
|
B:GLU46
|
4.1
|
28.3
|
1.0
|
O
|
A:PHE97
|
4.2
|
30.2
|
1.0
|
CA
|
B:TRP47
|
4.2
|
28.6
|
1.0
|
O
|
B:LEU45
|
4.4
|
25.2
|
1.0
|
CG
|
A:PHE97
|
4.5
|
29.1
|
1.0
|
O
|
B:TRP47
|
4.5
|
27.8
|
1.0
|
O
|
A:ARG95
|
4.6
|
29.4
|
1.0
|
CB
|
B:GLU46
|
4.6
|
29.2
|
1.0
|
C
|
A:PHE97
|
4.6
|
28.0
|
1.0
|
CG
|
B:GLU46
|
4.6
|
32.9
|
1.0
|
O
|
B:HOH561
|
4.8
|
47.3
|
1.0
|
N
|
A:THR96
|
4.8
|
28.1
|
1.0
|
N
|
B:GLU46
|
4.8
|
26.6
|
1.0
|
C
|
B:TRP47
|
4.9
|
28.4
|
1.0
|
C
|
B:LEU45
|
5.0
|
25.7
|
1.0
|
|
Magnesium binding site 2 out
of 7 in 1q9l
Go back to
Magnesium Binding Sites List in 1q9l
Magnesium binding site 2 out
of 7 in the S25-2 Fab Unliganded 2
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 2 of S25-2 Fab Unliganded 2 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Mg212
b:24.6
occ:1.00
|
OD2
|
D:ASP171
|
3.2
|
52.3
|
1.0
|
OD1
|
D:ASP171
|
3.2
|
50.4
|
1.0
|
CG
|
D:ASP171
|
3.4
|
48.3
|
1.0
|
O
|
D:HOH711
|
3.6
|
24.3
|
1.0
|
O
|
D:SER170
|
4.0
|
45.0
|
1.0
|
C
|
D:SER170
|
4.2
|
44.4
|
1.0
|
N
|
D:ASP171
|
4.5
|
43.8
|
1.0
|
CB
|
D:ASP171
|
4.6
|
44.7
|
1.0
|
CA
|
D:ASP171
|
4.7
|
43.5
|
1.0
|
CA
|
D:SER170
|
4.7
|
45.1
|
1.0
|
|
Magnesium binding site 3 out
of 7 in 1q9l
Go back to
Magnesium Binding Sites List in 1q9l
Magnesium binding site 3 out
of 7 in the S25-2 Fab Unliganded 2
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 3 of S25-2 Fab Unliganded 2 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg215
b:38.0
occ:1.00
|
OD1
|
A:ASP166
|
1.9
|
47.7
|
1.0
|
O
|
B:HOH303
|
2.4
|
43.6
|
1.0
|
O
|
A:HOH694
|
2.4
|
30.1
|
1.0
|
O
|
A:HOH701
|
2.6
|
48.2
|
1.0
|
CE1
|
B:HIS162
|
2.6
|
37.4
|
1.0
|
CG
|
A:ASP166
|
2.8
|
44.6
|
1.0
|
O
|
B:HOH695
|
2.8
|
31.3
|
1.0
|
NZ
|
A:LYS168
|
3.0
|
53.1
|
1.0
|
OD2
|
A:ASP166
|
3.2
|
43.2
|
1.0
|
NE2
|
B:HIS162
|
3.4
|
37.1
|
1.0
|
ND1
|
B:HIS162
|
3.6
|
39.0
|
1.0
|
O
|
B:HOH405
|
4.0
|
55.3
|
1.0
|
CB
|
A:ASP166
|
4.1
|
43.4
|
1.0
|
O
|
A:HOH355
|
4.3
|
39.4
|
1.0
|
CE
|
A:LYS168
|
4.3
|
54.5
|
1.0
|
ND2
|
A:ASN137
|
4.4
|
39.0
|
1.0
|
CD2
|
B:HIS162
|
4.6
|
36.7
|
1.0
|
O
|
A:HOH580
|
4.7
|
27.2
|
1.0
|
CG
|
B:HIS162
|
4.7
|
36.6
|
1.0
|
OD2
|
A:ASP169
|
4.9
|
42.4
|
1.0
|
|
Magnesium binding site 4 out
of 7 in 1q9l
Go back to
Magnesium Binding Sites List in 1q9l
Magnesium binding site 4 out
of 7 in the S25-2 Fab Unliganded 2
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 4 of S25-2 Fab Unliganded 2 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Mg216
b:19.7
occ:1.00
|
O
|
D:HOH504
|
2.6
|
24.0
|
1.0
|
N
|
C:PHE97
|
3.1
|
26.9
|
1.0
|
N
|
D:TRP47
|
3.1
|
26.0
|
1.0
|
O
|
D:HOH460
|
3.5
|
38.6
|
1.0
|
CA
|
C:THR96
|
3.5
|
27.8
|
1.0
|
OG1
|
C:THR96
|
3.7
|
30.0
|
1.0
|
CA
|
D:GLU46
|
3.8
|
25.3
|
1.0
|
CD2
|
C:PHE97
|
3.8
|
25.9
|
1.0
|
C
|
C:THR96
|
3.8
|
27.8
|
1.0
|
CB
|
C:THR96
|
3.8
|
27.5
|
1.0
|
CB
|
D:TRP47
|
3.8
|
26.4
|
1.0
|
C
|
D:GLU46
|
4.0
|
25.6
|
1.0
|
CA
|
D:TRP47
|
4.1
|
26.5
|
1.0
|
CA
|
C:PHE97
|
4.2
|
26.1
|
1.0
|
CB
|
C:PHE97
|
4.2
|
26.9
|
1.0
|
O
|
D:LEU45
|
4.3
|
23.9
|
1.0
|
O
|
C:PHE97
|
4.3
|
26.5
|
1.0
|
CG
|
C:PHE97
|
4.4
|
27.4
|
1.0
|
O
|
C:ARG95
|
4.5
|
27.2
|
1.0
|
O
|
C:HOH437
|
4.5
|
41.9
|
1.0
|
O
|
D:TRP47
|
4.5
|
27.2
|
1.0
|
N
|
C:THR96
|
4.6
|
27.6
|
1.0
|
CG
|
D:GLU46
|
4.7
|
30.7
|
1.0
|
CB
|
D:GLU46
|
4.7
|
26.1
|
1.0
|
C
|
C:PHE97
|
4.7
|
25.9
|
1.0
|
N
|
D:GLU46
|
4.7
|
24.7
|
1.0
|
CE2
|
C:PHE97
|
4.7
|
27.8
|
1.0
|
C
|
D:TRP47
|
4.8
|
27.7
|
1.0
|
C
|
D:LEU45
|
4.9
|
24.4
|
1.0
|
C
|
C:ARG95
|
4.9
|
29.3
|
1.0
|
|
Magnesium binding site 5 out
of 7 in 1q9l
Go back to
Magnesium Binding Sites List in 1q9l
Magnesium binding site 5 out
of 7 in the S25-2 Fab Unliganded 2
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 5 of S25-2 Fab Unliganded 2 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Mg217
b:29.9
occ:1.00
|
O
|
C:HOH631
|
2.3
|
36.1
|
1.0
|
NZ
|
C:LYS89
|
2.6
|
32.0
|
1.0
|
OD1
|
D:ASP95
|
2.6
|
58.6
|
1.0
|
CD
|
C:ARG95
|
3.3
|
35.4
|
1.0
|
CG
|
D:ASP95
|
3.5
|
59.8
|
1.0
|
NE
|
C:ARG95
|
3.5
|
37.2
|
1.0
|
CG
|
C:ARG95
|
3.5
|
35.4
|
1.0
|
CE
|
C:LYS89
|
3.6
|
33.0
|
1.0
|
CD
|
C:LYS89
|
3.8
|
30.7
|
1.0
|
OD2
|
D:ASP95
|
3.8
|
59.0
|
1.0
|
OG
|
D:SER35
|
4.1
|
30.4
|
1.0
|
CB
|
C:ARG95
|
4.2
|
32.5
|
1.0
|
CD1
|
D:TRP47
|
4.5
|
27.4
|
1.0
|
CB
|
D:SER35
|
4.5
|
29.9
|
1.0
|
NE1
|
D:TRP47
|
4.6
|
29.4
|
1.0
|
CB
|
D:ASP95
|
4.7
|
61.2
|
1.0
|
CZ
|
C:ARG95
|
4.7
|
36.9
|
1.0
|
O
|
C:HOH683
|
4.8
|
38.3
|
1.0
|
OH
|
C:TYR36
|
4.8
|
35.1
|
1.0
|
|
Magnesium binding site 6 out
of 7 in 1q9l
Go back to
Magnesium Binding Sites List in 1q9l
Magnesium binding site 6 out
of 7 in the S25-2 Fab Unliganded 2
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 6 of S25-2 Fab Unliganded 2 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Mg218
b:37.3
occ:1.00
|
OD1
|
C:ASP166
|
1.8
|
47.4
|
1.0
|
O
|
C:HOH314
|
2.0
|
34.1
|
1.0
|
NZ
|
C:LYS168
|
2.0
|
56.0
|
1.0
|
NE2
|
D:HIS162
|
2.2
|
41.1
|
1.0
|
O
|
D:HOH351
|
2.7
|
33.9
|
1.0
|
CG
|
C:ASP166
|
2.9
|
43.8
|
1.0
|
CD2
|
D:HIS162
|
3.0
|
40.7
|
1.0
|
CE1
|
D:HIS162
|
3.2
|
42.0
|
1.0
|
CE
|
C:LYS168
|
3.3
|
57.6
|
1.0
|
OD2
|
C:ASP166
|
3.4
|
41.2
|
1.0
|
ND2
|
C:ASN137
|
3.9
|
46.2
|
1.0
|
CD
|
C:LYS168
|
4.1
|
55.4
|
1.0
|
CB
|
C:ASP166
|
4.2
|
42.6
|
1.0
|
CG
|
D:HIS162
|
4.2
|
39.7
|
1.0
|
ND1
|
D:HIS162
|
4.3
|
41.3
|
1.0
|
O
|
D:HOH452
|
4.6
|
48.2
|
1.0
|
CG
|
C:LYS168
|
4.7
|
52.3
|
1.0
|
CG
|
C:ASN137
|
4.8
|
43.3
|
1.0
|
OD2
|
C:ASP169
|
4.9
|
38.1
|
1.0
|
OD1
|
C:ASN137
|
4.9
|
47.2
|
1.0
|
O
|
D:VAL161
|
4.9
|
35.0
|
1.0
|
O
|
C:HOH574
|
4.9
|
48.9
|
1.0
|
|
Magnesium binding site 7 out
of 7 in 1q9l
Go back to
Magnesium Binding Sites List in 1q9l
Magnesium binding site 7 out
of 7 in the S25-2 Fab Unliganded 2
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 7 of S25-2 Fab Unliganded 2 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Mg219
b:29.0
occ:1.00
|
OG
|
C:SER190
|
3.0
|
34.9
|
1.0
|
N
|
C:GLY151
|
3.2
|
47.3
|
1.0
|
OG1
|
C:THR192
|
3.3
|
33.4
|
1.0
|
O
|
C:LYS148
|
3.3
|
40.2
|
1.0
|
N
|
C:ASP150
|
3.4
|
42.4
|
1.0
|
CB
|
C:SER190
|
3.5
|
34.2
|
1.0
|
O
|
C:SER190
|
3.6
|
32.7
|
1.0
|
C
|
C:SER190
|
3.7
|
32.1
|
1.0
|
C
|
C:LYS148
|
3.8
|
40.3
|
1.0
|
CB
|
C:THR192
|
3.8
|
31.5
|
1.0
|
CA
|
C:ASP150
|
4.0
|
44.4
|
1.0
|
N
|
C:THR192
|
4.0
|
30.5
|
1.0
|
N
|
C:TYR191
|
4.0
|
32.0
|
1.0
|
C
|
C:ILE149
|
4.0
|
40.7
|
1.0
|
C
|
C:ASP150
|
4.1
|
46.4
|
1.0
|
CB
|
C:LYS148
|
4.1
|
41.1
|
1.0
|
CA
|
C:GLY151
|
4.1
|
49.8
|
1.0
|
N
|
C:ILE149
|
4.2
|
38.5
|
1.0
|
CA
|
C:SER190
|
4.2
|
32.3
|
1.0
|
CA
|
C:ILE149
|
4.2
|
38.5
|
1.0
|
C
|
C:TYR191
|
4.3
|
29.9
|
1.0
|
CA
|
C:TYR191
|
4.4
|
29.9
|
1.0
|
CA
|
C:THR192
|
4.6
|
31.9
|
1.0
|
CA
|
C:LYS148
|
4.6
|
40.9
|
1.0
|
O
|
C:ILE149
|
5.0
|
39.8
|
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 11:11:10 2024
|