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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:

Magnesium (Mg) 13 atoms

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

Go back to 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: Sat Dec 12 10:49:43 2020

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