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Cobalt in PDB 3rgt: Crystal Structure of D-Mannonate Dehydratase From Chromohalobacter Salexigens Complexed with D-Arabinohydroxamate

Enzymatic activity of Crystal Structure of D-Mannonate Dehydratase From Chromohalobacter Salexigens Complexed with D-Arabinohydroxamate

All present enzymatic activity of Crystal Structure of D-Mannonate Dehydratase From Chromohalobacter Salexigens Complexed with D-Arabinohydroxamate:
4.2.1.8;

Protein crystallography data

The structure of Crystal Structure of D-Mannonate Dehydratase From Chromohalobacter Salexigens Complexed with D-Arabinohydroxamate, PDB code: 3rgt 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) 39.85 / 1.90
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 110.712, 179.657, 85.422, 90.00, 90.00, 90.00
R / Rfree (%) 17.8 / 22.2

Cobalt Binding Sites:

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

Cobalt binding site 1 out of 4 in 3rgt

Go back to Cobalt Binding Sites List in 3rgt
Cobalt binding site 1 out of 4 in the Crystal Structure of D-Mannonate Dehydratase From Chromohalobacter Salexigens Complexed with D-Arabinohydroxamate


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 1 of Crystal Structure of D-Mannonate Dehydratase From Chromohalobacter Salexigens Complexed with D-Arabinohydroxamate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Co406

b:33.9
occ:1.00
 OE1 A:GLU239 2.1 30.6 1.0
OD2 A:ASP213 2.1 23.4 1.0
OAC A:EZ4407 2.1 30.7 1.0
OE1 A:GLU265 2.2 27.2 1.0
O A:HOH784 2.2 31.2 1.0
OAK A:EZ4407 2.3 35.5 1.0
NAD A:EZ4407 2.9 41.0 1.0
CAE A:EZ4407 2.9 37.9 1.0
CD A:GLU265 3.0 31.4 1.0
CD A:GLU239 3.1 34.4 1.0
CG A:ASP213 3.1 29.2 1.0
OE2 A:GLU265 3.2 27.3 1.0
OD1 A:ASP213 3.5 27.5 1.0
OE2 A:GLU239 3.8 31.8 1.0
NH2 A:ARG286 3.8 28.7 1.0
O A:HOH413 3.9 23.3 1.0
CD2 A:HIS215 4.0 34.9 1.0
O A:HOH427 4.1 27.7 1.0
CG A:GLU239 4.1 29.7 1.0
NE2 A:HIS215 4.2 33.9 1.0
OD2 A:ASP240 4.2 32.4 1.0
CAF A:EZ4407 4.4 46.6 1.0
CG A:GLU265 4.4 23.1 1.0
CB A:ASP213 4.4 28.1 1.0
NH1 A:ARG149 4.4 38.3 1.0
OH C:TYR77 4.6 28.5 1.0
CG A:ASP240 4.8 30.7 1.0
CZ A:ARG286 4.9 29.1 1.0
CD2 A:HIS315 4.9 24.8 1.0
NE A:ARG286 4.9 29.2 1.0
CAG A:EZ4407 4.9 44.7 1.0
NE2 A:HIS315 5.0 29.7 1.0
CB A:GLU265 5.0 25.6 1.0

Cobalt binding site 2 out of 4 in 3rgt

Go back to Cobalt Binding Sites List in 3rgt
Cobalt binding site 2 out of 4 in the Crystal Structure of D-Mannonate Dehydratase From Chromohalobacter Salexigens Complexed with D-Arabinohydroxamate


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 2 of Crystal Structure of D-Mannonate Dehydratase From Chromohalobacter Salexigens Complexed with D-Arabinohydroxamate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Co406

b:33.8
occ:1.00
 OD2 B:ASP213 2.1 26.5 1.0
OAC B:EZ4407 2.2 32.6 1.0
O B:HOH783 2.2 25.3 1.0
OE1 B:GLU265 2.2 25.6 1.0
OE1 B:GLU239 2.2 25.6 1.0
OAK B:EZ4407 2.3 25.6 1.0
NAD B:EZ4407 2.8 38.4 1.0
CAE B:EZ4407 2.9 35.6 1.0
CD B:GLU265 3.0 33.3 1.0
CG B:ASP213 3.1 31.3 1.0
CD B:GLU239 3.2 30.1 1.0
OE2 B:GLU265 3.2 26.4 1.0
OD1 B:ASP213 3.4 26.1 1.0
NH2 B:ARG286 3.7 28.8 1.0
OE2 B:GLU239 3.8 30.8 1.0
CD2 B:HIS215 3.9 31.8 1.0
O B:HOH408 4.0 28.4 1.0
O B:HOH410 4.1 27.3 1.0
OD2 B:ASP240 4.1 25.5 1.0
CG B:GLU239 4.2 29.4 1.0
NE2 B:HIS215 4.2 34.6 1.0
CAF B:EZ4407 4.4 45.8 1.0
CG B:GLU265 4.4 25.0 1.0
CB B:ASP213 4.4 28.9 1.0
NH1 B:ARG149 4.5 31.0 1.0
OH D:TYR77 4.6 24.7 1.0
OH B:TYR161 4.6 45.8 1.0
CZ B:ARG286 4.7 26.1 1.0
CG B:ASP240 4.7 28.9 1.0
NE B:ARG286 4.9 27.0 1.0
CAG B:EZ4407 4.9 38.4 1.0
CD2 B:HIS315 5.0 26.6 1.0
CB B:GLU265 5.0 28.7 1.0

Cobalt binding site 3 out of 4 in 3rgt

Go back to Cobalt Binding Sites List in 3rgt
Cobalt binding site 3 out of 4 in the Crystal Structure of D-Mannonate Dehydratase From Chromohalobacter Salexigens Complexed with D-Arabinohydroxamate


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 3 of Crystal Structure of D-Mannonate Dehydratase From Chromohalobacter Salexigens Complexed with D-Arabinohydroxamate within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Co406

b:33.0
occ:1.00
 OD2 C:ASP213 2.1 22.7 1.0
OE1 C:GLU239 2.1 26.5 1.0
O C:HOH782 2.2 24.7 1.0
OE1 C:GLU265 2.2 22.6 1.0
OAK C:EZ4407 2.2 30.9 1.0
OAC C:EZ4407 2.3 26.3 1.0
CAE C:EZ4407 2.9 37.2 1.0
NAD C:EZ4407 2.9 32.0 1.0
CD C:GLU265 3.0 27.8 1.0
CG C:ASP213 3.1 31.4 1.0
CD C:GLU239 3.1 25.6 1.0
OE2 C:GLU265 3.2 23.9 1.0
OD1 C:ASP213 3.4 24.8 1.0
OE2 C:GLU239 3.8 27.4 1.0
O C:HOH412 3.8 28.3 1.0
CD2 C:HIS215 3.9 31.0 1.0
NH2 C:ARG286 3.9 27.0 1.0
OD2 C:ASP240 4.1 26.2 1.0
CG C:GLU239 4.1 28.4 1.0
O C:HOH409 4.2 25.0 1.0
NE2 C:HIS215 4.2 37.9 1.0
NH1 C:ARG149 4.2 33.7 1.0
CB C:ASP213 4.4 29.1 1.0
CAF C:EZ4407 4.4 44.7 1.0
CG C:GLU265 4.4 26.0 1.0
OH A:TYR77 4.7 27.3 1.0
CG C:ASP240 4.7 29.1 1.0
CZ C:ARG286 4.9 27.2 1.0
NE C:ARG286 5.0 25.7 1.0
CAG C:EZ4407 5.0 40.8 1.0

Cobalt binding site 4 out of 4 in 3rgt

Go back to Cobalt Binding Sites List in 3rgt
Cobalt binding site 4 out of 4 in the Crystal Structure of D-Mannonate Dehydratase From Chromohalobacter Salexigens Complexed with D-Arabinohydroxamate


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 4 of Crystal Structure of D-Mannonate Dehydratase From Chromohalobacter Salexigens Complexed with D-Arabinohydroxamate within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Co406

b:34.7
occ:1.00
 OE1 D:GLU239 2.1 28.4 1.0
OD2 D:ASP213 2.2 22.0 1.0
O D:HOH781 2.2 27.7 1.0
OAC D:EZ4407 2.2 34.2 1.0
OE1 D:GLU265 2.2 25.1 1.0
OAK D:EZ4407 2.2 34.8 1.0
CAE D:EZ4407 2.9 41.7 1.0
NAD D:EZ4407 2.9 35.7 1.0
CD D:GLU265 3.0 32.9 1.0
CG D:ASP213 3.1 31.1 1.0
CD D:GLU239 3.1 30.2 1.0
OE2 D:GLU265 3.2 30.3 1.0
OD1 D:ASP213 3.4 23.6 1.0
OE2 D:GLU239 3.8 27.5 1.0
O D:HOH409 3.9 29.7 1.0
NH2 D:ARG286 4.0 26.7 1.0
CD2 D:HIS215 4.0 31.0 1.0
CG D:GLU239 4.0 25.7 1.0
NE2 D:HIS215 4.1 37.6 1.0
OD2 D:ASP240 4.2 31.4 1.0
O D:HOH410 4.3 25.9 1.0
NH1 D:ARG149 4.3 39.1 1.0
CAF D:EZ4407 4.4 43.9 1.0
CB D:ASP213 4.4 28.0 1.0
CG D:GLU265 4.4 28.8 1.0
OH B:TYR77 4.6 32.3 1.0
CG D:ASP240 4.7 29.3 1.0
CAG D:EZ4407 4.9 47.9 1.0
CZ D:ARG286 5.0 31.6 1.0
CB D:GLU265 5.0 21.8 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 D-Arabinohydroxamate To Be Published.
Page generated: Tue Jul 30 16:33:37 2024

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