Chlorine in PDB 9qcg: Crystal Structure of Methanopyrus Kandleri Malate Dehydrogenase Mutant 4 at Room Temperature
Enzymatic activity of Crystal Structure of Methanopyrus Kandleri Malate Dehydrogenase Mutant 4 at Room Temperature
All present enzymatic activity of Crystal Structure of Methanopyrus Kandleri Malate Dehydrogenase Mutant 4 at Room Temperature:
1.1.1.299;
Protein crystallography data
The structure of Crystal Structure of Methanopyrus Kandleri Malate Dehydrogenase Mutant 4 at Room Temperature, PDB code: 9qcg
was solved by
S.Coquille,
D.Madern,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
17.90 /
2.39
|
Space group
|
P 41 21 2
|
Cell size a, b, c (Å), α, β, γ (°)
|
75.305,
75.305,
270.065,
90,
90,
90
|
R / Rfree (%)
|
26.3 /
30.9
|
Other elements in 9qcg:
The structure of Crystal Structure of Methanopyrus Kandleri Malate Dehydrogenase Mutant 4 at Room Temperature also contains other interesting chemical elements:
Chlorine Binding Sites:
The binding sites of Chlorine atom in the Crystal Structure of Methanopyrus Kandleri Malate Dehydrogenase Mutant 4 at Room Temperature
(pdb code 9qcg). This binding sites where shown within
5.0 Angstroms radius around Chlorine atom.
In total 3 binding sites of Chlorine where determined in the
Crystal Structure of Methanopyrus Kandleri Malate Dehydrogenase Mutant 4 at Room Temperature, PDB code: 9qcg:
Jump to Chlorine binding site number:
1;
2;
3;
Chlorine binding site 1 out
of 3 in 9qcg
Go back to
Chlorine Binding Sites List in 9qcg
Chlorine binding site 1 out
of 3 in the Crystal Structure of Methanopyrus Kandleri Malate Dehydrogenase Mutant 4 at Room Temperature
 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 Methanopyrus Kandleri Malate Dehydrogenase Mutant 4 at Room Temperature within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cl402
b:40.5
occ:1.00
|
HE
|
B:ARG20
|
2.4
|
50.3
|
1.0
|
HE
|
A:ARG20
|
2.5
|
33.0
|
1.0
|
HH21
|
A:ARG20
|
2.7
|
42.1
|
1.0
|
HH21
|
B:ARG20
|
2.8
|
43.0
|
1.0
|
HG23
|
A:THR16
|
3.0
|
45.5
|
1.0
|
HE1
|
B:PHE230
|
3.1
|
35.1
|
1.0
|
HG23
|
B:THR16
|
3.1
|
47.2
|
1.0
|
HE1
|
A:PHE230
|
3.2
|
40.5
|
1.0
|
NE
|
B:ARG20
|
3.2
|
41.9
|
1.0
|
NE
|
A:ARG20
|
3.3
|
27.4
|
1.0
|
HD1
|
A:PHE230
|
3.4
|
57.0
|
1.0
|
HD1
|
B:PHE230
|
3.4
|
57.5
|
1.0
|
NH2
|
A:ARG20
|
3.5
|
35.0
|
1.0
|
NH2
|
B:ARG20
|
3.5
|
35.7
|
1.0
|
HG3
|
B:ARG20
|
3.6
|
43.6
|
1.0
|
CE1
|
B:PHE230
|
3.8
|
29.2
|
1.0
|
HG3
|
A:ARG20
|
3.8
|
66.7
|
1.0
|
HG22
|
B:THR16
|
3.8
|
47.2
|
1.0
|
CG2
|
A:THR16
|
3.8
|
37.9
|
1.0
|
CE1
|
A:PHE230
|
3.8
|
33.7
|
1.0
|
CZ
|
B:ARG20
|
3.9
|
38.1
|
1.0
|
HG22
|
A:THR16
|
3.9
|
45.5
|
1.0
|
CZ
|
A:ARG20
|
3.9
|
35.0
|
1.0
|
CG2
|
B:THR16
|
3.9
|
39.3
|
1.0
|
CD1
|
A:PHE230
|
3.9
|
47.4
|
1.0
|
CD1
|
B:PHE230
|
4.0
|
47.8
|
1.0
|
HG2
|
B:ARG20
|
4.0
|
43.6
|
1.0
|
HG21
|
A:THR16
|
4.1
|
45.5
|
1.0
|
HG2
|
A:ARG20
|
4.1
|
66.7
|
1.0
|
CG
|
B:ARG20
|
4.2
|
36.2
|
1.0
|
HG21
|
B:THR16
|
4.2
|
47.2
|
1.0
|
HH22
|
A:ARG20
|
4.2
|
42.1
|
1.0
|
CD
|
B:ARG20
|
4.3
|
27.9
|
1.0
|
HH22
|
B:ARG20
|
4.3
|
43.0
|
1.0
|
CG
|
A:ARG20
|
4.3
|
55.5
|
1.0
|
CD
|
A:ARG20
|
4.4
|
39.5
|
1.0
|
HB3
|
B:ALA19
|
4.5
|
46.8
|
1.0
|
HB3
|
A:ALA19
|
4.5
|
39.0
|
1.0
|
HA
|
B:THR16
|
4.6
|
40.2
|
1.0
|
HA
|
A:THR16
|
4.6
|
48.4
|
1.0
|
HD2
|
B:ARG20
|
4.7
|
33.5
|
1.0
|
HD2
|
A:ARG20
|
4.8
|
47.5
|
1.0
|
O
|
B:HOH501
|
4.9
|
56.7
|
1.0
|
HB1
|
B:ALA19
|
5.0
|
46.8
|
1.0
|
HD3
|
B:ARG20
|
5.0
|
33.5
|
1.0
|
|
Chlorine binding site 2 out
of 3 in 9qcg
Go back to
Chlorine Binding Sites List in 9qcg
Chlorine binding site 2 out
of 3 in the Crystal Structure of Methanopyrus Kandleri Malate Dehydrogenase Mutant 4 at Room Temperature
 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 Methanopyrus Kandleri Malate Dehydrogenase Mutant 4 at Room Temperature within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cl403
b:63.0
occ:0.80
|
H
|
A:THR252
|
2.6
|
58.0
|
1.0
|
HA
|
A:LEU251
|
3.0
|
40.2
|
1.0
|
HB2
|
A:SER152
|
3.1
|
61.0
|
1.0
|
O
|
A:HOH523
|
3.2
|
54.9
|
1.0
|
OG1
|
A:THR252
|
3.3
|
49.3
|
1.0
|
ND1
|
A:HIS149
|
3.3
|
48.0
|
1.0
|
N
|
A:THR252
|
3.3
|
48.2
|
1.0
|
HG1
|
A:THR252
|
3.4
|
59.2
|
1.0
|
HA
|
A:HIS149
|
3.4
|
52.1
|
1.0
|
HD22
|
A:LEU251
|
3.7
|
43.5
|
1.0
|
HG
|
A:SER152
|
3.7
|
66.7
|
1.0
|
HB3
|
A:LEU251
|
3.7
|
37.9
|
1.0
|
HB
|
A:THR252
|
3.8
|
60.0
|
1.0
|
CB
|
A:SER152
|
3.8
|
50.8
|
1.0
|
HB3
|
A:SER152
|
3.8
|
61.0
|
1.0
|
CA
|
A:LEU251
|
3.8
|
33.5
|
1.0
|
HE1
|
A:HIS149
|
3.9
|
60.0
|
1.0
|
CB
|
A:THR252
|
3.9
|
49.9
|
1.0
|
HH12
|
A:ARG173
|
4.0
|
68.9
|
1.0
|
CE1
|
A:HIS149
|
4.0
|
50.0
|
1.0
|
C
|
A:LEU251
|
4.1
|
45.2
|
1.0
|
OG
|
A:SER152
|
4.2
|
55.5
|
1.0
|
O
|
A:HIS149
|
4.2
|
46.6
|
1.0
|
CA
|
A:THR252
|
4.2
|
45.6
|
1.0
|
CB
|
A:LEU251
|
4.3
|
31.5
|
1.0
|
CA
|
A:HIS149
|
4.3
|
43.4
|
1.0
|
HD23
|
A:LEU251
|
4.4
|
43.5
|
1.0
|
CG
|
A:HIS149
|
4.4
|
44.8
|
1.0
|
CD2
|
A:LEU251
|
4.4
|
36.1
|
1.0
|
NH1
|
A:ARG173
|
4.5
|
57.3
|
1.0
|
O
|
A:VAL250
|
4.6
|
44.2
|
1.0
|
HH11
|
A:ARG173
|
4.6
|
68.9
|
1.0
|
HB2
|
A:HIS149
|
4.7
|
42.0
|
1.0
|
C
|
A:HIS149
|
4.7
|
36.4
|
1.0
|
CB
|
A:HIS149
|
4.8
|
35.0
|
1.0
|
SD
|
A:MET153
|
4.8
|
57.2
|
1.0
|
HA
|
A:ARG173
|
4.8
|
62.3
|
1.0
|
HB3
|
A:ARG173
|
4.8
|
65.6
|
1.0
|
O
|
A:THR172
|
4.9
|
47.5
|
1.0
|
O
|
A:THR252
|
4.9
|
45.5
|
1.0
|
HA
|
A:THR252
|
5.0
|
54.8
|
1.0
|
HB2
|
A:ARG173
|
5.0
|
65.6
|
1.0
|
CG
|
A:LEU251
|
5.0
|
32.5
|
1.0
|
|
Chlorine binding site 3 out
of 3 in 9qcg
Go back to
Chlorine Binding Sites List in 9qcg
Chlorine binding site 3 out
of 3 in the Crystal Structure of Methanopyrus Kandleri Malate Dehydrogenase Mutant 4 at Room Temperature
 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 Methanopyrus Kandleri Malate Dehydrogenase Mutant 4 at Room Temperature within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Cl402
b:57.3
occ:1.00
|
H
|
B:THR252
|
2.6
|
54.4
|
1.0
|
HG1
|
B:THR252
|
2.7
|
76.7
|
1.0
|
HB2
|
B:SER152
|
3.0
|
51.9
|
1.0
|
OG1
|
B:THR252
|
3.0
|
63.9
|
1.0
|
HA
|
B:LEU251
|
3.2
|
48.0
|
1.0
|
N
|
B:THR252
|
3.3
|
45.3
|
1.0
|
ND1
|
B:HIS149
|
3.4
|
41.2
|
1.0
|
HA
|
B:HIS149
|
3.5
|
44.5
|
1.0
|
HB
|
B:THR252
|
3.6
|
62.1
|
1.0
|
HG
|
B:SER152
|
3.6
|
49.8
|
1.0
|
CB
|
B:SER152
|
3.7
|
43.2
|
1.0
|
HB3
|
B:SER152
|
3.7
|
51.9
|
1.0
|
CB
|
B:THR252
|
3.7
|
51.7
|
1.0
|
HH11
|
B:ARG173
|
3.9
|
69.8
|
1.0
|
HB3
|
B:LEU251
|
3.9
|
32.7
|
1.0
|
HE1
|
B:HIS149
|
3.9
|
53.8
|
1.0
|
HD22
|
B:LEU251
|
3.9
|
41.3
|
1.0
|
CA
|
B:LEU251
|
3.9
|
40.0
|
1.0
|
HH12
|
B:ARG173
|
4.0
|
69.8
|
1.0
|
OG
|
B:SER152
|
4.0
|
41.4
|
1.0
|
CE1
|
B:HIS149
|
4.0
|
44.8
|
1.0
|
HG3
|
B:ARG173
|
4.1
|
63.9
|
1.0
|
C
|
B:LEU251
|
4.1
|
45.6
|
1.0
|
CA
|
B:THR252
|
4.1
|
42.1
|
1.0
|
NH1
|
B:ARG173
|
4.2
|
58.1
|
1.0
|
O
|
B:HIS149
|
4.2
|
37.7
|
1.0
|
HG2
|
B:MET153
|
4.3
|
50.5
|
1.0
|
CA
|
B:HIS149
|
4.4
|
37.0
|
1.0
|
CB
|
B:LEU251
|
4.4
|
27.1
|
1.0
|
CG
|
B:HIS149
|
4.5
|
41.6
|
1.0
|
HD23
|
B:LEU251
|
4.7
|
41.3
|
1.0
|
CD2
|
B:LEU251
|
4.7
|
34.3
|
1.0
|
O
|
B:VAL250
|
4.7
|
43.3
|
1.0
|
C
|
B:HIS149
|
4.8
|
29.1
|
1.0
|
O
|
B:THR252
|
4.8
|
52.7
|
1.0
|
HB2
|
B:HIS149
|
4.8
|
44.1
|
1.0
|
CB
|
B:HIS149
|
4.8
|
36.7
|
1.0
|
HA
|
B:THR252
|
4.9
|
50.6
|
1.0
|
HA
|
B:ARG173
|
4.9
|
64.8
|
1.0
|
C
|
B:THR252
|
5.0
|
40.1
|
1.0
|
O
|
B:THR172
|
5.0
|
43.6
|
1.0
|
|
Reference:
S.Coquille,
C.S.Pereira,
J.Roche,
G.Santoni,
S.Engilberge,
C.Brochier-Armanet,
E.Girard,
F.Sterpone,
D.Madern.
Allostery and Evolution: A Molecular Journey Through the Structural and Dynamical Landscape of An Enzyme Super Family. Mol.Biol.Evol. V. 42 2025.
ISSN: ESSN 1537-1719
PubMed: 39834309
DOI: 10.1093/MOLBEV/MSAE265
Page generated: Sun Jul 13 17:20:05 2025
|