Chlorine in PDB 4k2s: Crystal Structure of the Mutant P317A of D-Mannonate Dehydratase From Chromohalobacter Salexigens Complexed with Mg and D-Gluconate
Enzymatic activity of Crystal Structure of the Mutant P317A of D-Mannonate Dehydratase From Chromohalobacter Salexigens Complexed with Mg and D-Gluconate
All present enzymatic activity of Crystal Structure of the Mutant P317A of D-Mannonate Dehydratase From Chromohalobacter Salexigens Complexed with Mg and D-Gluconate:
4.2.1.8;
Protein crystallography data
The structure of Crystal Structure of the Mutant P317A of D-Mannonate Dehydratase From Chromohalobacter Salexigens Complexed with Mg and D-Gluconate, PDB code: 4k2s
was solved by
A.A.Fedorov,
E.V.Fedorov,
D.Wichelecki,
J.A.Gerlt,
S.C.Almo,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
44.25 /
1.70
|
Space group
|
C 1 2 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
196.334,
85.790,
195.638,
90.00,
110.47,
90.00
|
R / Rfree (%)
|
16.9 /
20.3
|
Other elements in 4k2s:
The structure of Crystal Structure of the Mutant P317A of D-Mannonate Dehydratase From Chromohalobacter Salexigens Complexed with Mg and D-Gluconate also contains other interesting chemical elements:
Chlorine Binding Sites:
The binding sites of Chlorine atom in the Crystal Structure of the Mutant P317A of D-Mannonate Dehydratase From Chromohalobacter Salexigens Complexed with Mg and D-Gluconate
(pdb code 4k2s). 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 the Mutant P317A of D-Mannonate Dehydratase From Chromohalobacter Salexigens Complexed with Mg and D-Gluconate, PDB code: 4k2s:
Jump to Chlorine binding site number:
1;
2;
3;
4;
5;
6;
Chlorine binding site 1 out
of 6 in 4k2s
Go back to
Chlorine Binding Sites List in 4k2s
Chlorine binding site 1 out
of 6 in the Crystal Structure of the Mutant P317A of D-Mannonate Dehydratase From Chromohalobacter Salexigens Complexed with Mg and D-Gluconate
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 the Mutant P317A of D-Mannonate Dehydratase From Chromohalobacter Salexigens Complexed with Mg and D-Gluconate within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cl503
b:18.9
occ:1.00
|
N
|
A:VAL83
|
3.3
|
10.2
|
1.0
|
N
|
B:VAL83
|
3.4
|
11.7
|
1.0
|
CD
|
A:PRO82
|
3.6
|
11.5
|
1.0
|
CD
|
B:PRO82
|
3.6
|
11.3
|
1.0
|
CB
|
A:VAL83
|
3.6
|
11.2
|
1.0
|
CB
|
B:VAL83
|
3.6
|
11.9
|
1.0
|
N
|
A:PRO82
|
3.7
|
9.6
|
1.0
|
N
|
B:PRO82
|
3.7
|
12.0
|
1.0
|
OG1
|
A:THR84
|
3.7
|
10.3
|
1.0
|
CA
|
A:GLY81
|
3.7
|
9.2
|
1.0
|
OG1
|
B:THR84
|
3.8
|
9.6
|
1.0
|
C
|
A:GLY81
|
3.8
|
8.8
|
1.0
|
CA
|
B:GLY81
|
3.8
|
10.3
|
1.0
|
N
|
A:THR84
|
3.8
|
9.5
|
1.0
|
C
|
B:GLY81
|
3.8
|
11.1
|
1.0
|
N
|
B:THR84
|
3.9
|
8.4
|
1.0
|
CG2
|
B:VAL83
|
3.9
|
10.3
|
1.0
|
CG2
|
A:VAL83
|
3.9
|
9.0
|
1.0
|
CA
|
A:VAL83
|
4.0
|
8.7
|
1.0
|
CA
|
B:VAL83
|
4.0
|
13.1
|
1.0
|
CG
|
B:PRO82
|
4.1
|
15.4
|
1.0
|
CG
|
A:PRO82
|
4.2
|
12.8
|
1.0
|
C
|
A:PRO82
|
4.3
|
12.9
|
1.0
|
C
|
B:PRO82
|
4.4
|
10.7
|
1.0
|
C
|
A:VAL83
|
4.4
|
10.3
|
1.0
|
O
|
A:GLY81
|
4.5
|
8.6
|
1.0
|
C
|
B:VAL83
|
4.5
|
11.7
|
1.0
|
O
|
B:ARG80
|
4.5
|
8.8
|
1.0
|
O
|
B:GLY81
|
4.5
|
9.4
|
1.0
|
CB
|
A:THR84
|
4.5
|
13.3
|
1.0
|
CA
|
A:PRO82
|
4.5
|
10.9
|
1.0
|
CA
|
B:PRO82
|
4.5
|
7.8
|
1.0
|
O
|
A:ARG80
|
4.5
|
10.0
|
1.0
|
CB
|
B:THR84
|
4.6
|
11.1
|
1.0
|
CA
|
A:THR84
|
4.8
|
11.2
|
1.0
|
CG1
|
A:VAL83
|
4.9
|
11.1
|
1.0
|
CA
|
B:THR84
|
4.9
|
8.3
|
1.0
|
CG1
|
B:VAL83
|
4.9
|
9.3
|
1.0
|
N
|
A:GLY81
|
5.0
|
9.5
|
1.0
|
CB
|
B:PRO82
|
5.0
|
11.0
|
1.0
|
N
|
B:GLY81
|
5.0
|
9.4
|
1.0
|
|
Chlorine binding site 2 out
of 6 in 4k2s
Go back to
Chlorine Binding Sites List in 4k2s
Chlorine binding site 2 out
of 6 in the Crystal Structure of the Mutant P317A of D-Mannonate Dehydratase From Chromohalobacter Salexigens Complexed with Mg and D-Gluconate
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 the Mutant P317A of D-Mannonate Dehydratase From Chromohalobacter Salexigens Complexed with Mg and D-Gluconate within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Cl504
b:20.9
occ:1.00
|
N
|
H:VAL83
|
3.3
|
11.6
|
1.0
|
N
|
D:VAL83
|
3.4
|
11.0
|
1.0
|
N
|
H:PRO82
|
3.6
|
10.6
|
1.0
|
CD
|
H:PRO82
|
3.6
|
14.0
|
1.0
|
CB
|
D:VAL83
|
3.7
|
14.2
|
1.0
|
CB
|
H:VAL83
|
3.7
|
12.1
|
1.0
|
CA
|
H:GLY81
|
3.7
|
10.5
|
1.0
|
C
|
H:GLY81
|
3.7
|
14.1
|
1.0
|
OG1
|
H:THR84
|
3.7
|
15.7
|
1.0
|
N
|
H:THR84
|
3.7
|
11.4
|
1.0
|
N
|
D:PRO82
|
3.7
|
15.0
|
1.0
|
CD
|
D:PRO82
|
3.7
|
13.2
|
1.0
|
C
|
D:GLY81
|
3.8
|
11.3
|
1.0
|
CA
|
D:GLY81
|
3.8
|
10.3
|
1.0
|
CA
|
H:VAL83
|
3.9
|
11.6
|
1.0
|
CG2
|
H:VAL83
|
3.9
|
12.0
|
1.0
|
CG2
|
D:VAL83
|
3.9
|
13.4
|
1.0
|
N
|
D:THR84
|
3.9
|
11.4
|
1.0
|
OG1
|
D:THR84
|
3.9
|
17.0
|
1.0
|
CA
|
D:VAL83
|
4.0
|
12.1
|
1.0
|
CG
|
H:PRO82
|
4.1
|
16.9
|
1.0
|
CG
|
D:PRO82
|
4.2
|
15.1
|
1.0
|
C
|
H:PRO82
|
4.2
|
13.5
|
1.0
|
C
|
H:VAL83
|
4.4
|
16.1
|
1.0
|
C
|
D:PRO82
|
4.4
|
10.9
|
1.0
|
O
|
H:GLY81
|
4.4
|
12.7
|
1.0
|
CA
|
H:PRO82
|
4.4
|
14.7
|
1.0
|
CB
|
H:THR84
|
4.4
|
18.2
|
1.0
|
O
|
H:ARG80
|
4.4
|
11.4
|
1.0
|
O
|
D:GLY81
|
4.5
|
10.7
|
1.0
|
CA
|
D:PRO82
|
4.6
|
12.4
|
1.0
|
C
|
D:VAL83
|
4.6
|
11.1
|
1.0
|
O
|
D:ARG80
|
4.6
|
11.3
|
1.0
|
CA
|
H:THR84
|
4.7
|
13.5
|
1.0
|
CB
|
D:THR84
|
4.7
|
11.7
|
1.0
|
N
|
H:GLY81
|
4.9
|
12.7
|
1.0
|
CB
|
H:PRO82
|
4.9
|
17.5
|
1.0
|
CG1
|
D:VAL83
|
4.9
|
12.1
|
1.0
|
CB
|
D:PRO82
|
5.0
|
13.5
|
1.0
|
CA
|
D:THR84
|
5.0
|
11.9
|
1.0
|
CG1
|
H:VAL83
|
5.0
|
12.3
|
1.0
|
|
Chlorine binding site 3 out
of 6 in 4k2s
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Chlorine Binding Sites List in 4k2s
Chlorine binding site 3 out
of 6 in the Crystal Structure of the Mutant P317A of D-Mannonate Dehydratase From Chromohalobacter Salexigens Complexed with Mg and D-Gluconate
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 the Mutant P317A of D-Mannonate Dehydratase From Chromohalobacter Salexigens Complexed with Mg and D-Gluconate within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Cl504
b:24.5
occ:1.00
|
N
|
C:VAL83
|
3.4
|
15.8
|
1.0
|
N
|
E:VAL83
|
3.4
|
10.3
|
1.0
|
CD
|
E:PRO82
|
3.4
|
13.7
|
1.0
|
CB
|
C:VAL83
|
3.6
|
14.7
|
1.0
|
OG1
|
C:THR84
|
3.6
|
14.9
|
1.0
|
CB
|
E:VAL83
|
3.6
|
11.1
|
1.0
|
N
|
E:PRO82
|
3.7
|
10.6
|
1.0
|
CA
|
C:GLY81
|
3.7
|
11.3
|
1.0
|
C
|
C:GLY81
|
3.7
|
13.6
|
1.0
|
N
|
C:PRO82
|
3.7
|
11.8
|
1.0
|
N
|
C:THR84
|
3.7
|
14.9
|
1.0
|
CD
|
C:PRO82
|
3.7
|
12.9
|
1.0
|
CA
|
E:GLY81
|
3.8
|
13.9
|
1.0
|
C
|
E:GLY81
|
3.8
|
11.4
|
1.0
|
CG2
|
E:VAL83
|
3.8
|
11.2
|
1.0
|
CG2
|
C:VAL83
|
4.0
|
13.3
|
1.0
|
CA
|
C:VAL83
|
4.0
|
16.1
|
1.0
|
N
|
E:THR84
|
4.0
|
12.2
|
1.0
|
OG1
|
E:THR84
|
4.0
|
14.6
|
1.0
|
CA
|
E:VAL83
|
4.0
|
10.7
|
1.0
|
CG
|
C:PRO82
|
4.2
|
15.0
|
1.0
|
O
|
C:GLY81
|
4.3
|
12.7
|
1.0
|
C
|
C:PRO82
|
4.3
|
14.6
|
1.0
|
O
|
C:ARG80
|
4.4
|
13.1
|
1.0
|
C
|
E:PRO82
|
4.4
|
13.1
|
1.0
|
CG
|
E:PRO82
|
4.4
|
16.3
|
1.0
|
CB
|
C:THR84
|
4.4
|
15.6
|
1.0
|
C
|
C:VAL83
|
4.4
|
14.9
|
1.0
|
CA
|
E:PRO82
|
4.5
|
11.0
|
1.0
|
CA
|
C:PRO82
|
4.5
|
13.2
|
1.0
|
O
|
E:GLY81
|
4.6
|
10.7
|
1.0
|
C
|
E:VAL83
|
4.6
|
12.9
|
1.0
|
O
|
E:ARG80
|
4.6
|
13.7
|
1.0
|
CA
|
C:THR84
|
4.7
|
12.2
|
1.0
|
CB
|
E:PRO82
|
4.8
|
16.0
|
1.0
|
CB
|
E:THR84
|
4.8
|
17.1
|
1.0
|
N
|
C:GLY81
|
4.9
|
11.0
|
1.0
|
CG1
|
C:VAL83
|
4.9
|
13.4
|
1.0
|
CG1
|
E:VAL83
|
4.9
|
11.5
|
1.0
|
CB
|
C:PRO82
|
5.0
|
14.9
|
1.0
|
|
Chlorine binding site 4 out
of 6 in 4k2s
Go back to
Chlorine Binding Sites List in 4k2s
Chlorine binding site 4 out
of 6 in the Crystal Structure of the Mutant P317A of D-Mannonate Dehydratase From Chromohalobacter Salexigens Complexed with Mg and D-Gluconate
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 the Mutant P317A of D-Mannonate Dehydratase From Chromohalobacter Salexigens Complexed with Mg and D-Gluconate within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Cl505
b:45.5
occ:1.00
|
O
|
E:HOH711
|
3.0
|
21.2
|
1.0
|
O
|
E:HOH683
|
3.1
|
14.7
|
1.0
|
N
|
E:GLU398
|
3.2
|
19.9
|
1.0
|
O
|
E:TRP184
|
3.3
|
15.7
|
1.0
|
CB
|
E:LEU397
|
3.5
|
12.9
|
1.0
|
OE1
|
E:GLU398
|
3.5
|
39.1
|
1.0
|
CG
|
E:GLU398
|
3.7
|
32.8
|
1.0
|
CB
|
E:GLU398
|
3.8
|
25.9
|
1.0
|
CA
|
E:LEU397
|
3.9
|
13.2
|
1.0
|
O
|
H:HOH804
|
4.0
|
28.6
|
1.0
|
C
|
E:LEU397
|
4.0
|
17.1
|
1.0
|
CD2
|
E:LEU397
|
4.0
|
13.2
|
1.0
|
CD
|
E:GLU398
|
4.1
|
38.6
|
1.0
|
CA
|
E:GLU398
|
4.1
|
21.5
|
1.0
|
O
|
H:HOH739
|
4.1
|
26.8
|
1.0
|
CG
|
E:LEU397
|
4.2
|
13.2
|
1.0
|
CA
|
E:SER185
|
4.2
|
12.8
|
1.0
|
O
|
E:HOH718
|
4.3
|
24.1
|
1.0
|
C
|
E:TRP184
|
4.4
|
15.2
|
1.0
|
CD1
|
E:LEU397
|
4.5
|
14.9
|
1.0
|
CB
|
E:SER185
|
4.7
|
15.6
|
1.0
|
O
|
E:HOH729
|
4.8
|
22.2
|
1.0
|
N
|
E:SER185
|
4.8
|
14.3
|
1.0
|
N
|
E:ASP399
|
4.9
|
17.6
|
1.0
|
|
Chlorine binding site 5 out
of 6 in 4k2s
Go back to
Chlorine Binding Sites List in 4k2s
Chlorine binding site 5 out
of 6 in the Crystal Structure of the Mutant P317A of D-Mannonate Dehydratase From Chromohalobacter Salexigens Complexed with Mg and D-Gluconate
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 the Mutant P317A of D-Mannonate Dehydratase From Chromohalobacter Salexigens Complexed with Mg and D-Gluconate within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:Cl503
b:19.2
occ:1.00
|
N
|
G:VAL83
|
3.3
|
10.6
|
1.0
|
N
|
F:VAL83
|
3.4
|
12.6
|
1.0
|
CD
|
G:PRO82
|
3.5
|
11.1
|
1.0
|
N
|
G:PRO82
|
3.6
|
7.8
|
1.0
|
CB
|
G:VAL83
|
3.6
|
8.9
|
1.0
|
CB
|
F:VAL83
|
3.6
|
9.2
|
1.0
|
N
|
F:PRO82
|
3.7
|
8.3
|
1.0
|
OG1
|
F:THR84
|
3.7
|
12.4
|
1.0
|
CD
|
F:PRO82
|
3.7
|
8.0
|
1.0
|
CA
|
G:GLY81
|
3.8
|
7.5
|
1.0
|
C
|
G:GLY81
|
3.8
|
10.6
|
1.0
|
CA
|
F:GLY81
|
3.8
|
12.8
|
1.0
|
C
|
F:GLY81
|
3.8
|
8.6
|
1.0
|
N
|
F:THR84
|
3.8
|
10.9
|
1.0
|
N
|
G:THR84
|
3.8
|
8.2
|
1.0
|
OG1
|
G:THR84
|
3.8
|
13.9
|
1.0
|
CG2
|
G:VAL83
|
3.9
|
11.9
|
1.0
|
CA
|
G:VAL83
|
3.9
|
9.1
|
1.0
|
CA
|
F:VAL83
|
4.0
|
11.4
|
1.0
|
CG2
|
F:VAL83
|
4.0
|
11.3
|
1.0
|
CG
|
G:PRO82
|
4.1
|
14.3
|
1.0
|
C
|
G:PRO82
|
4.3
|
11.1
|
1.0
|
CG
|
F:PRO82
|
4.3
|
8.7
|
1.0
|
C
|
F:PRO82
|
4.4
|
12.0
|
1.0
|
C
|
F:VAL83
|
4.4
|
10.7
|
1.0
|
O
|
F:ARG80
|
4.4
|
9.7
|
1.0
|
CA
|
G:PRO82
|
4.4
|
7.8
|
1.0
|
C
|
G:VAL83
|
4.4
|
10.6
|
1.0
|
O
|
F:GLY81
|
4.5
|
8.9
|
1.0
|
O
|
G:GLY81
|
4.5
|
10.6
|
1.0
|
CB
|
F:THR84
|
4.5
|
11.2
|
1.0
|
CA
|
F:PRO82
|
4.6
|
10.9
|
1.0
|
CB
|
G:THR84
|
4.6
|
9.8
|
1.0
|
O
|
G:ARG80
|
4.6
|
8.0
|
1.0
|
CA
|
F:THR84
|
4.8
|
13.4
|
1.0
|
CA
|
G:THR84
|
4.9
|
9.3
|
1.0
|
CG1
|
G:VAL83
|
4.9
|
10.0
|
1.0
|
CB
|
G:PRO82
|
4.9
|
11.7
|
1.0
|
CG1
|
F:VAL83
|
4.9
|
9.6
|
1.0
|
N
|
F:GLY81
|
4.9
|
10.7
|
1.0
|
N
|
G:GLY81
|
5.0
|
10.9
|
1.0
|
|
Chlorine binding site 6 out
of 6 in 4k2s
Go back to
Chlorine Binding Sites List in 4k2s
Chlorine binding site 6 out
of 6 in the Crystal Structure of the Mutant P317A of D-Mannonate Dehydratase From Chromohalobacter Salexigens Complexed with Mg and D-Gluconate
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 the Mutant P317A of D-Mannonate Dehydratase From Chromohalobacter Salexigens Complexed with Mg and D-Gluconate within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:Cl504
b:45.4
occ:1.00
|
ND1
|
G:HIS52
|
2.7
|
11.0
|
1.0
|
O
|
F:HOH667
|
2.9
|
15.0
|
1.0
|
OG
|
F:SER391
|
3.1
|
26.8
|
1.0
|
O
|
F:GLY40
|
3.3
|
12.9
|
1.0
|
CE1
|
G:HIS52
|
3.4
|
11.3
|
1.0
|
CG
|
F:ARG389
|
3.5
|
34.4
|
1.0
|
O
|
F:ALA390
|
3.6
|
21.8
|
1.0
|
CD
|
F:ARG389
|
3.7
|
40.5
|
1.0
|
CG
|
G:HIS52
|
3.9
|
10.7
|
1.0
|
C
|
F:GLY40
|
3.9
|
11.8
|
1.0
|
C
|
F:ALA390
|
3.9
|
16.9
|
1.0
|
CA
|
F:GLY40
|
4.1
|
12.2
|
1.0
|
O
|
G:HOH702
|
4.1
|
18.1
|
1.0
|
CB
|
F:SER391
|
4.2
|
19.6
|
1.0
|
CA
|
F:SER391
|
4.2
|
13.8
|
1.0
|
N
|
F:SER391
|
4.3
|
14.3
|
1.0
|
N
|
F:ALA390
|
4.3
|
14.9
|
1.0
|
CB
|
G:HIS52
|
4.3
|
10.7
|
1.0
|
O
|
G:GLU51
|
4.3
|
15.7
|
1.0
|
OH
|
F:TYR387
|
4.4
|
17.3
|
1.0
|
CA
|
G:HIS52
|
4.4
|
12.3
|
1.0
|
NE2
|
G:HIS52
|
4.6
|
13.2
|
1.0
|
OE1
|
F:GLU42
|
4.7
|
14.2
|
1.0
|
CB
|
F:ARG389
|
4.7
|
28.7
|
1.0
|
O
|
F:SER177
|
4.7
|
35.2
|
1.0
|
CA
|
F:ALA390
|
4.7
|
18.0
|
1.0
|
NH1
|
F:ARG41
|
4.8
|
14.4
|
1.0
|
CD2
|
G:HIS52
|
4.9
|
11.8
|
1.0
|
OE2
|
G:GLU51
|
4.9
|
33.0
|
1.0
|
N
|
F:ARG41
|
4.9
|
11.5
|
1.0
|
CA
|
F:ARG389
|
5.0
|
21.5
|
1.0
|
C
|
F:ARG389
|
5.0
|
13.5
|
1.0
|
|
Reference:
A.A.Fedorov,
E.V.Fedorov,
D.Wichelecki,
J.A.Gerlt,
S.C.Almo.
Crystal Structure of the Mutant P317A of D-Mannonate Dehydratase From Chromohalobacter Salexigens Complexed with Mg and D-Gluconate To Be Published.
Page generated: Sun Jul 21 17:56:09 2024
|