Atomistry » Cobalt » PDB 3r86-3ura » 3rgt
Atomistry »
  Cobalt »
    PDB 3r86-3ura »
      3rgt »

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: Sun Jul 13 19:18:54 2025

Last articles

Fe in 2YXO
Fe in 2YRS
Fe in 2YXC
Fe in 2YNM
Fe in 2YVJ
Fe in 2YP1
Fe in 2YU2
Fe in 2YU1
Fe in 2YQB
Fe in 2YOO
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy