Chlorine in PDB 1yjx: Crystal Structure of Human B Type Phosphoglycerate Mutase
Enzymatic activity of Crystal Structure of Human B Type Phosphoglycerate Mutase
All present enzymatic activity of Crystal Structure of Human B Type Phosphoglycerate Mutase:
3.1.3.13;
5.4.2.1;
5.4.2.4;
Protein crystallography data
The structure of Crystal Structure of Human B Type Phosphoglycerate Mutase, PDB code: 1yjx
was solved by
Y.Wang,
Z.Wei,
L.Liu,
W.Gong,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
29.91 /
2.80
|
Space group
|
P 1 21 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
130.534,
75.931,
186.978,
90.00,
94.42,
90.00
|
R / Rfree (%)
|
23.3 /
27.2
|
Chlorine Binding Sites:
The binding sites of Chlorine atom in the Crystal Structure of Human B Type Phosphoglycerate Mutase
(pdb code 1yjx). This binding sites where shown within
5.0 Angstroms radius around Chlorine atom.
In total 6 binding sites of Chlorine where determined in the
Crystal Structure of Human B Type Phosphoglycerate Mutase, PDB code: 1yjx:
Jump to Chlorine binding site number:
1;
2;
3;
4;
5;
6;
Chlorine binding site 1 out
of 6 in 1yjx
Go back to
Chlorine Binding Sites List in 1yjx
Chlorine binding site 1 out
of 6 in the Crystal Structure of Human B Type Phosphoglycerate Mutase
Mono view
Stereo pair view
|
A full contact list of Chlorine with other atoms in the Cl binding
site number 1 of Crystal Structure of Human B Type Phosphoglycerate Mutase within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cl263
b:22.2
occ:1.00
|
NH2
|
A:ARG83
|
2.9
|
17.5
|
1.0
|
NH2
|
B:ARG83
|
3.1
|
18.9
|
1.0
|
NE1
|
A:TRP68
|
3.2
|
21.7
|
1.0
|
NE1
|
B:TRP68
|
3.2
|
21.8
|
1.0
|
NH1
|
A:ARG83
|
3.4
|
20.3
|
1.0
|
CZ
|
A:ARG83
|
3.6
|
18.9
|
1.0
|
NH1
|
B:ARG83
|
3.6
|
19.7
|
1.0
|
CG2
|
B:VAL81
|
3.7
|
18.7
|
1.0
|
CG2
|
A:VAL81
|
3.8
|
17.4
|
1.0
|
CZ
|
B:ARG83
|
3.8
|
19.2
|
1.0
|
CG1
|
B:VAL81
|
3.8
|
17.4
|
1.0
|
CE2
|
A:TRP68
|
4.0
|
22.0
|
1.0
|
CG1
|
A:VAL81
|
4.0
|
17.9
|
1.0
|
CD1
|
B:TRP68
|
4.1
|
21.1
|
1.0
|
CE2
|
B:TRP68
|
4.1
|
21.2
|
1.0
|
CD1
|
A:TRP68
|
4.1
|
22.2
|
1.0
|
CZ2
|
A:TRP68
|
4.2
|
20.5
|
1.0
|
CZ2
|
B:TRP68
|
4.4
|
21.1
|
1.0
|
CB
|
B:VAL81
|
4.4
|
17.8
|
1.0
|
CB
|
A:VAL81
|
4.6
|
19.2
|
1.0
|
NE
|
A:ARG83
|
4.9
|
19.2
|
1.0
|
|
Chlorine binding site 2 out
of 6 in 1yjx
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Chlorine Binding Sites List in 1yjx
Chlorine binding site 2 out
of 6 in the Crystal Structure of Human B Type Phosphoglycerate Mutase
Mono view
Stereo pair view
|
A full contact list of Chlorine with other atoms in the Cl binding
site number 2 of Crystal Structure of Human B Type Phosphoglycerate Mutase within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Cl263
b:23.4
occ:1.00
|
NH2
|
D:ARG83
|
2.9
|
20.4
|
1.0
|
NE1
|
D:TRP68
|
3.1
|
22.7
|
1.0
|
NH2
|
C:ARG83
|
3.1
|
21.1
|
1.0
|
NE1
|
C:TRP68
|
3.2
|
21.4
|
1.0
|
NH1
|
D:ARG83
|
3.5
|
22.6
|
1.0
|
NH1
|
C:ARG83
|
3.6
|
21.2
|
1.0
|
CZ
|
D:ARG83
|
3.7
|
20.8
|
1.0
|
CZ
|
C:ARG83
|
3.8
|
21.9
|
1.0
|
CG2
|
C:VAL81
|
3.8
|
20.7
|
1.0
|
CG2
|
D:VAL81
|
3.8
|
18.2
|
1.0
|
CG1
|
C:VAL81
|
3.9
|
18.3
|
1.0
|
CE2
|
D:TRP68
|
3.9
|
24.0
|
1.0
|
CD1
|
D:TRP68
|
4.0
|
22.5
|
1.0
|
CE2
|
C:TRP68
|
4.0
|
22.9
|
1.0
|
CD1
|
C:TRP68
|
4.0
|
22.9
|
1.0
|
CG1
|
D:VAL81
|
4.1
|
18.7
|
1.0
|
CZ2
|
D:TRP68
|
4.1
|
23.1
|
1.0
|
CZ2
|
C:TRP68
|
4.3
|
23.0
|
1.0
|
CB
|
C:VAL81
|
4.5
|
19.3
|
1.0
|
CB
|
D:VAL81
|
4.6
|
18.6
|
1.0
|
NE
|
D:ARG83
|
5.0
|
20.3
|
1.0
|
|
Chlorine binding site 3 out
of 6 in 1yjx
Go back to
Chlorine Binding Sites List in 1yjx
Chlorine binding site 3 out
of 6 in the Crystal Structure of Human B Type Phosphoglycerate Mutase
Mono view
Stereo pair view
|
A full contact list of Chlorine with other atoms in the Cl binding
site number 3 of Crystal Structure of Human B Type Phosphoglycerate Mutase within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:Cl263
b:31.7
occ:1.00
|
NH2
|
F:ARG83
|
3.0
|
19.2
|
1.0
|
NH2
|
E:ARG83
|
3.1
|
20.5
|
1.0
|
NE1
|
F:TRP68
|
3.2
|
23.5
|
1.0
|
NE1
|
E:TRP68
|
3.3
|
24.3
|
1.0
|
NH1
|
F:ARG83
|
3.5
|
19.0
|
1.0
|
NH1
|
E:ARG83
|
3.5
|
22.2
|
1.0
|
CZ
|
F:ARG83
|
3.7
|
19.4
|
1.0
|
CG2
|
F:VAL81
|
3.7
|
21.7
|
1.0
|
CZ
|
E:ARG83
|
3.7
|
20.5
|
1.0
|
CG2
|
E:VAL81
|
3.8
|
19.4
|
1.0
|
CG1
|
E:VAL81
|
3.9
|
20.3
|
1.0
|
CG1
|
F:VAL81
|
4.0
|
20.8
|
1.0
|
CE2
|
F:TRP68
|
4.0
|
22.7
|
1.0
|
CD1
|
F:TRP68
|
4.1
|
22.8
|
1.0
|
CE2
|
E:TRP68
|
4.2
|
24.2
|
1.0
|
CD1
|
E:TRP68
|
4.2
|
24.5
|
1.0
|
CZ2
|
F:TRP68
|
4.3
|
22.6
|
1.0
|
CZ2
|
E:TRP68
|
4.4
|
24.3
|
1.0
|
CB
|
F:VAL81
|
4.5
|
21.0
|
1.0
|
CB
|
E:VAL81
|
4.5
|
21.5
|
1.0
|
NE
|
F:ARG83
|
5.0
|
19.8
|
1.0
|
|
Chlorine binding site 4 out
of 6 in 1yjx
Go back to
Chlorine Binding Sites List in 1yjx
Chlorine binding site 4 out
of 6 in the Crystal Structure of Human B Type Phosphoglycerate Mutase
Mono view
Stereo pair view
|
A full contact list of Chlorine with other atoms in the Cl binding
site number 4 of Crystal Structure of Human B Type Phosphoglycerate Mutase within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
H:Cl263
b:25.9
occ:1.00
|
NH2
|
H:ARG83
|
2.9
|
24.6
|
1.0
|
NH2
|
G:ARG83
|
3.1
|
21.8
|
1.0
|
NE1
|
G:TRP68
|
3.2
|
22.7
|
1.0
|
NE1
|
H:TRP68
|
3.2
|
25.8
|
1.0
|
NH1
|
H:ARG83
|
3.5
|
25.0
|
1.0
|
NH1
|
G:ARG83
|
3.6
|
22.5
|
1.0
|
CZ
|
H:ARG83
|
3.6
|
24.0
|
1.0
|
CG2
|
G:VAL81
|
3.7
|
20.2
|
1.0
|
CG2
|
H:VAL81
|
3.8
|
20.6
|
1.0
|
CZ
|
G:ARG83
|
3.8
|
23.6
|
1.0
|
CG1
|
G:VAL81
|
3.8
|
19.9
|
1.0
|
CE2
|
H:TRP68
|
4.0
|
25.3
|
1.0
|
CG1
|
H:VAL81
|
4.0
|
19.7
|
1.0
|
CD1
|
G:TRP68
|
4.1
|
23.2
|
1.0
|
CE2
|
G:TRP68
|
4.1
|
23.1
|
1.0
|
CD1
|
H:TRP68
|
4.1
|
24.2
|
1.0
|
CZ2
|
H:TRP68
|
4.2
|
24.4
|
1.0
|
CZ2
|
G:TRP68
|
4.4
|
23.8
|
1.0
|
CB
|
G:VAL81
|
4.4
|
20.5
|
1.0
|
CB
|
H:VAL81
|
4.5
|
20.9
|
1.0
|
NE
|
H:ARG83
|
4.9
|
21.9
|
1.0
|
|
Chlorine binding site 5 out
of 6 in 1yjx
Go back to
Chlorine Binding Sites List in 1yjx
Chlorine binding site 5 out
of 6 in the Crystal Structure of Human B Type Phosphoglycerate Mutase
Mono view
Stereo pair view
|
A full contact list of Chlorine with other atoms in the Cl binding
site number 5 of Crystal Structure of Human B Type Phosphoglycerate Mutase within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
J:Cl263
b:32.8
occ:1.00
|
NH2
|
J:ARG83
|
3.0
|
20.3
|
1.0
|
NH2
|
I:ARG83
|
3.1
|
20.1
|
1.0
|
NH1
|
I:ARG83
|
3.3
|
19.1
|
1.0
|
NE1
|
J:TRP68
|
3.3
|
25.8
|
1.0
|
NH1
|
J:ARG83
|
3.4
|
23.9
|
1.0
|
CG2
|
J:VAL81
|
3.5
|
18.4
|
1.0
|
CG2
|
I:VAL81
|
3.6
|
21.6
|
1.0
|
NE1
|
I:TRP68
|
3.6
|
23.9
|
1.0
|
CZ
|
J:ARG83
|
3.6
|
22.3
|
1.0
|
CZ
|
I:ARG83
|
3.6
|
19.6
|
1.0
|
CG1
|
J:VAL81
|
3.8
|
17.6
|
1.0
|
CG1
|
I:VAL81
|
3.9
|
17.7
|
1.0
|
CE2
|
J:TRP68
|
4.2
|
25.8
|
1.0
|
CD1
|
J:TRP68
|
4.2
|
24.4
|
1.0
|
CB
|
J:VAL81
|
4.3
|
20.2
|
1.0
|
CB
|
I:VAL81
|
4.3
|
20.8
|
1.0
|
CE2
|
I:TRP68
|
4.4
|
23.5
|
1.0
|
CD1
|
I:TRP68
|
4.5
|
24.5
|
1.0
|
CZ2
|
J:TRP68
|
4.5
|
26.0
|
1.0
|
CZ2
|
I:TRP68
|
4.6
|
23.7
|
1.0
|
NE
|
J:ARG83
|
4.9
|
21.2
|
1.0
|
NE
|
I:ARG83
|
4.9
|
20.0
|
1.0
|
|
Chlorine binding site 6 out
of 6 in 1yjx
Go back to
Chlorine Binding Sites List in 1yjx
Chlorine binding site 6 out
of 6 in the Crystal Structure of Human B Type Phosphoglycerate Mutase
Mono view
Stereo pair view
|
A full contact list of Chlorine with other atoms in the Cl binding
site number 6 of Crystal Structure of Human B Type Phosphoglycerate Mutase within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
K:Cl263
b:21.9
occ:1.00
|
NH2
|
L:ARG83
|
3.1
|
20.0
|
1.0
|
NH2
|
K:ARG83
|
3.1
|
19.8
|
1.0
|
NH1
|
L:ARG83
|
3.4
|
20.5
|
1.0
|
NH1
|
K:ARG83
|
3.4
|
21.6
|
1.0
|
NE1
|
L:TRP68
|
3.4
|
23.3
|
1.0
|
NE1
|
K:TRP68
|
3.4
|
23.9
|
1.0
|
CG2
|
L:VAL81
|
3.6
|
17.5
|
1.0
|
CG2
|
K:VAL81
|
3.6
|
18.2
|
1.0
|
CZ
|
L:ARG83
|
3.7
|
20.5
|
1.0
|
CZ
|
K:ARG83
|
3.7
|
21.0
|
1.0
|
CG1
|
K:VAL81
|
3.8
|
15.5
|
1.0
|
CG1
|
L:VAL81
|
3.8
|
18.2
|
1.0
|
CE2
|
L:TRP68
|
4.3
|
22.9
|
1.0
|
CE2
|
K:TRP68
|
4.3
|
23.2
|
1.0
|
CD1
|
K:TRP68
|
4.3
|
24.2
|
1.0
|
CB
|
K:VAL81
|
4.3
|
19.0
|
1.0
|
CD1
|
L:TRP68
|
4.3
|
22.2
|
1.0
|
CB
|
L:VAL81
|
4.3
|
18.5
|
1.0
|
CZ2
|
L:TRP68
|
4.5
|
22.6
|
1.0
|
CZ2
|
K:TRP68
|
4.5
|
21.9
|
1.0
|
NE
|
L:ARG83
|
5.0
|
19.1
|
1.0
|
|
Reference:
Y.Wang,
Z.Wei,
L.Liu,
Z.Cheng,
Y.Lin,
F.Ji,
W.Gong.
Crystal Structure of Human B-Type Phosphoglycerate Mutase Bound with Citrate. Biochem.Biophys.Res.Commun. V. 331 1207 2005.
ISSN: ISSN 0006-291X
PubMed: 15883004
DOI: 10.1016/J.BBRC.2005.03.243
Page generated: Sat Jul 20 04:21:59 2024
|