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Chlorine in PDB 4kpl: Crystal Structure of D-Mannonate Dehydratase From Chromohalobacter Salexigens Complexed with Mg,D-Mannonate and 2-Keto-3-Deoxy-D- Gluconate

Enzymatic activity of Crystal Structure of D-Mannonate Dehydratase From Chromohalobacter Salexigens Complexed with Mg,D-Mannonate and 2-Keto-3-Deoxy-D- Gluconate

All present enzymatic activity of Crystal Structure of D-Mannonate Dehydratase From Chromohalobacter Salexigens Complexed with Mg,D-Mannonate and 2-Keto-3-Deoxy-D- Gluconate:
4.2.1.8;

Protein crystallography data

The structure of Crystal Structure of D-Mannonate Dehydratase From Chromohalobacter Salexigens Complexed with Mg,D-Mannonate and 2-Keto-3-Deoxy-D- Gluconate, PDB code: 4kpl 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) 41.82 / 2.00
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 110.242, 167.263, 168.863, 90.00, 90.00, 90.00
R / Rfree (%) 17.3 / 22.3

Other elements in 4kpl:

The structure of Crystal Structure of D-Mannonate Dehydratase From Chromohalobacter Salexigens Complexed with Mg,D-Mannonate and 2-Keto-3-Deoxy-D- Gluconate also contains other interesting chemical elements:

Magnesium (Mg) 8 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Crystal Structure of D-Mannonate Dehydratase From Chromohalobacter Salexigens Complexed with Mg,D-Mannonate and 2-Keto-3-Deoxy-D- Gluconate (pdb code 4kpl). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 4 binding sites of Chlorine where determined in the Crystal Structure of D-Mannonate Dehydratase From Chromohalobacter Salexigens Complexed with Mg,D-Mannonate and 2-Keto-3-Deoxy-D- Gluconate, PDB code: 4kpl:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in 4kpl

Go back to Chlorine Binding Sites List in 4kpl
Chlorine binding site 1 out of 4 in the Crystal Structure of D-Mannonate Dehydratase From Chromohalobacter Salexigens Complexed with Mg,D-Mannonate and 2-Keto-3-Deoxy-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 D-Mannonate Dehydratase From Chromohalobacter Salexigens Complexed with Mg,D-Mannonate and 2-Keto-3-Deoxy-D- Gluconate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl502

b:22.3
occ:1.00
 N E:VAL83 3.4 12.0 1.0
N A:VAL83 3.4 19.0 1.0
CD A:PRO82 3.5 12.3 1.0
CB E:VAL83 3.6 18.7 1.0
N A:PRO82 3.6 13.6 1.0
OG1 E:THR84 3.7 10.3 1.0
N E:PRO82 3.7 15.0 1.0
CB A:VAL83 3.7 15.8 1.0
CD E:PRO82 3.7 10.5 1.0
C E:GLY81 3.7 16.8 1.0
N E:THR84 3.8 16.9 1.0
CA E:GLY81 3.8 15.5 1.0
CG2 E:VAL83 3.8 19.2 1.0
CA A:GLY81 3.8 8.7 1.0
C A:GLY81 3.8 15.4 1.0
CG2 A:VAL83 3.8 10.8 1.0
N A:THR84 3.9 13.2 1.0
OG1 A:THR84 4.0 18.2 1.0
CA E:VAL83 4.0 16.9 1.0
CA A:VAL83 4.1 15.3 1.0
CG E:PRO82 4.1 15.8 1.0
C E:PRO82 4.3 12.8 1.0
O E:GLY81 4.4 12.3 1.0
C A:PRO82 4.4 16.0 1.0
CB E:THR84 4.4 11.2 1.0
C E:VAL83 4.4 21.1 1.0
CA A:PRO82 4.5 15.5 1.0
CA E:PRO82 4.5 15.5 1.0
O E:ARG80 4.5 14.8 1.0
O A:GLY81 4.5 15.8 1.0
CG A:PRO82 4.5 20.3 1.0
C A:VAL83 4.5 12.7 1.0
CB A:THR84 4.6 20.6 1.0
O A:ARG80 4.6 10.3 1.0
CA E:THR84 4.7 16.2 1.0
CB A:PRO82 4.8 15.2 1.0
CA A:THR84 4.9 18.1 1.0
CB E:PRO82 4.9 15.0 1.0
N E:GLY81 4.9 11.1 1.0
CG1 E:VAL83 4.9 8.4 1.0
CG1 A:VAL83 5.0 12.5 1.0

Chlorine binding site 2 out of 4 in 4kpl

Go back to Chlorine Binding Sites List in 4kpl
Chlorine binding site 2 out of 4 in the Crystal Structure of D-Mannonate Dehydratase From Chromohalobacter Salexigens Complexed with Mg,D-Mannonate and 2-Keto-3-Deoxy-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 D-Mannonate Dehydratase From Chromohalobacter Salexigens Complexed with Mg,D-Mannonate and 2-Keto-3-Deoxy-D- Gluconate within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl502

b:27.2
occ:1.00
 CD C:PRO82 3.3 25.4 1.0
N C:VAL83 3.4 14.1 1.0
N G:VAL83 3.4 15.3 1.0
CD G:PRO82 3.5 17.0 1.0
CB G:VAL83 3.6 12.3 1.0
N C:PRO82 3.6 20.0 1.0
CB C:VAL83 3.6 13.4 1.0
CG2 C:VAL83 3.7 14.5 1.0
N G:PRO82 3.7 11.1 1.0
OG1 G:THR84 3.7 18.8 1.0
N G:THR84 3.8 12.1 1.0
CA G:GLY81 3.8 9.1 1.0
C C:GLY81 3.8 19.7 1.0
C G:GLY81 3.8 10.0 1.0
CA C:GLY81 3.8 18.2 1.0
N C:THR84 3.9 13.2 1.0
CG2 G:VAL83 3.9 12.0 1.0
CA G:VAL83 4.0 13.2 1.0
OG1 C:THR84 4.0 19.3 1.0
CA C:VAL83 4.0 15.7 1.0
O G:ARG80 4.3 15.5 1.0
C C:PRO82 4.4 13.4 1.0
C G:PRO82 4.4 15.9 1.0
C G:VAL83 4.4 13.5 1.0
CG C:PRO82 4.4 24.6 1.0
CA C:PRO82 4.5 16.8 1.0
O C:GLY81 4.5 17.3 1.0
O G:GLY81 4.5 12.5 1.0
C C:VAL83 4.5 17.0 1.0
CB G:THR84 4.5 18.0 1.0
CA G:PRO82 4.6 12.5 1.0
O C:ARG80 4.6 20.5 1.0
CG G:PRO82 4.6 25.3 1.0
CB C:THR84 4.6 15.5 1.0
CB C:PRO82 4.8 16.3 1.0
CA G:THR84 4.8 13.6 1.0
CB G:PRO82 4.9 16.0 1.0
CA C:THR84 4.9 13.1 1.0
N G:GLY81 4.9 8.8 1.0
CG1 G:VAL83 4.9 10.1 1.0
CG1 C:VAL83 5.0 10.6 1.0

Chlorine binding site 3 out of 4 in 4kpl

Go back to Chlorine Binding Sites List in 4kpl
Chlorine binding site 3 out of 4 in the Crystal Structure of D-Mannonate Dehydratase From Chromohalobacter Salexigens Complexed with Mg,D-Mannonate and 2-Keto-3-Deoxy-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 D-Mannonate Dehydratase From Chromohalobacter Salexigens Complexed with Mg,D-Mannonate and 2-Keto-3-Deoxy-D- Gluconate within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl502

b:22.4
occ:1.00
 N B:VAL83 3.4 13.8 1.0
N D:VAL83 3.4 10.8 1.0
CD D:PRO82 3.4 18.0 1.0
CB B:VAL83 3.6 15.9 1.0
CA D:GLY81 3.7 12.6 1.0
CB D:VAL83 3.7 11.7 1.0
N B:PRO82 3.7 9.4 1.0
N D:PRO82 3.7 16.2 1.0
N B:THR84 3.7 16.2 1.0
CD B:PRO82 3.7 13.0 1.0
CG2 B:VAL83 3.7 12.9 1.0
C B:GLY81 3.7 13.4 1.0
CA B:GLY81 3.8 15.0 1.0
C D:GLY81 3.8 14.1 1.0
OG1 B:THR84 3.9 13.9 1.0
OG1 D:THR84 3.9 16.5 1.0
CG2 D:VAL83 3.9 10.2 1.0
N D:THR84 3.9 15.7 1.0
CA B:VAL83 4.0 15.7 1.0
CA D:VAL83 4.0 9.3 1.0
CG B:PRO82 4.2 10.3 1.0
C B:PRO82 4.3 13.4 1.0
CB B:THR84 4.4 13.9 1.0
O B:ARG80 4.4 11.2 1.0
O B:GLY81 4.4 13.8 1.0
C D:PRO82 4.4 16.5 1.0
C B:VAL83 4.4 15.4 1.0
CG D:PRO82 4.5 18.8 1.0
CA D:PRO82 4.5 18.1 1.0
CA B:PRO82 4.5 7.6 1.0
C D:VAL83 4.5 17.0 1.0
O D:ARG80 4.6 15.4 1.0
CB D:THR84 4.6 14.8 1.0
O D:GLY81 4.6 15.3 1.0
CA B:THR84 4.7 17.6 1.0
CB D:PRO82 4.7 17.1 1.0
CA D:THR84 4.9 15.6 1.0
N D:GLY81 4.9 11.7 1.0
N B:GLY81 4.9 12.2 1.0
CG1 B:VAL83 5.0 12.1 1.0

Chlorine binding site 4 out of 4 in 4kpl

Go back to Chlorine Binding Sites List in 4kpl
Chlorine binding site 4 out of 4 in the Crystal Structure of D-Mannonate Dehydratase From Chromohalobacter Salexigens Complexed with Mg,D-Mannonate and 2-Keto-3-Deoxy-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 D-Mannonate Dehydratase From Chromohalobacter Salexigens Complexed with Mg,D-Mannonate and 2-Keto-3-Deoxy-D- Gluconate within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Cl502

b:23.7
occ:1.00
 N H:VAL83 3.3 16.9 1.0
N F:VAL83 3.5 11.8 1.0
CB H:VAL83 3.5 16.9 1.0
CD F:PRO82 3.6 13.9 1.0
CA H:GLY81 3.6 13.0 1.0
N H:PRO82 3.6 16.7 1.0
CB F:VAL83 3.6 19.2 1.0
N H:THR84 3.7 15.6 1.0
CD H:PRO82 3.7 16.9 1.0
CG2 F:VAL83 3.7 19.6 1.0
C H:GLY81 3.8 13.3 1.0
CA F:GLY81 3.8 16.0 1.0
N F:PRO82 3.8 11.4 1.0
OG1 H:THR84 3.8 20.1 1.0
C F:GLY81 3.9 16.3 1.0
CG2 H:VAL83 3.9 15.9 1.0
CA H:VAL83 3.9 22.4 1.0
N F:THR84 3.9 12.9 1.0
OG1 F:THR84 4.0 19.6 1.0
CA F:VAL83 4.1 14.9 1.0
CG H:PRO82 4.2 15.2 1.0
C H:PRO82 4.3 16.5 1.0
C H:VAL83 4.4 20.7 1.0
CB H:THR84 4.4 22.8 1.0
O H:ARG80 4.4 16.4 1.0
C F:PRO82 4.5 15.5 1.0
CA H:PRO82 4.5 14.4 1.0
O F:ARG80 4.5 15.6 1.0
O H:GLY81 4.5 12.5 1.0
C F:VAL83 4.5 17.5 1.0
CG F:PRO82 4.6 20.4 1.0
O F:GLY81 4.6 18.8 1.0
CB F:THR84 4.6 15.3 1.0
CA F:PRO82 4.6 17.4 1.0
CA H:THR84 4.7 11.6 1.0
CG1 H:VAL83 4.8 18.9 1.0
N H:GLY81 4.9 9.7 1.0
CB F:PRO82 4.9 18.0 1.0
CA F:THR84 4.9 13.0 1.0
CB H:PRO82 4.9 11.0 1.0
N F:GLY81 5.0 11.2 1.0
CG1 F:VAL83 5.0 12.3 1.0

Reference:

A.A.Fedorov, E.V.Fedorov, D.Wichelecki, J.A.Gerlt, S.C.Almo. Crystal Structure of D-Mannonate Dehydratase From Chromohalobacter Salexigens Complexed with Mg,D-Mannonate and 2-Keto-3-Deoxy-D-Gluconate To Be Published.
Page generated: Sun Jul 21 18:21:13 2024

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