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Cobalt in PDB 5esr: Crystal Structure of Haloalkane Dehalogenase (Dcca) From Caulobacter Crescentus

Enzymatic activity of Crystal Structure of Haloalkane Dehalogenase (Dcca) From Caulobacter Crescentus

All present enzymatic activity of Crystal Structure of Haloalkane Dehalogenase (Dcca) From Caulobacter Crescentus:
3.8.1.5;

Protein crystallography data

The structure of Crystal Structure of Haloalkane Dehalogenase (Dcca) From Caulobacter Crescentus, PDB code: 5esr was solved by V.N.Malashkevich, R.Toro, E.C.Mundorff, S.C.Almo, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.38 / 1.48
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 79.377, 79.643, 94.766, 90.00, 90.00, 90.00
R / Rfree (%) 12.6 / 14.9

Other elements in 5esr:

The structure of Crystal Structure of Haloalkane Dehalogenase (Dcca) From Caulobacter Crescentus also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms
Chlorine (Cl) 1 atom

Cobalt Binding Sites:

The binding sites of Cobalt atom in the Crystal Structure of Haloalkane Dehalogenase (Dcca) From Caulobacter Crescentus (pdb code 5esr). This binding sites where shown within 5.0 Angstroms radius around Cobalt atom.
In total 6 binding sites of Cobalt where determined in the Crystal Structure of Haloalkane Dehalogenase (Dcca) From Caulobacter Crescentus, PDB code: 5esr:
Jump to Cobalt binding site number: 1; 2; 3; 4; 5; 6;

Cobalt binding site 1 out of 6 in 5esr

Go back to Cobalt Binding Sites List in 5esr
Cobalt binding site 1 out of 6 in the Crystal Structure of Haloalkane Dehalogenase (Dcca) From Caulobacter Crescentus


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 Haloalkane Dehalogenase (Dcca) From Caulobacter Crescentus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Co401

b:5.2
occ:1.00
 NE2 A:HIS305 2.1 5.0 1.0
NE2 A:HIS303 2.1 5.8 1.0
OD1 A:ASP238 2.1 5.0 1.0
O A:HOH720 2.2 5.4 1.0
OD2 A:ASP238 2.2 5.7 1.0
CG A:ASP238 2.5 5.1 1.0
CE1 A:HIS305 3.0 4.8 1.0
CE1 A:HIS303 3.0 6.5 1.0
CD2 A:HIS305 3.1 5.1 1.0
CD2 A:HIS303 3.1 6.1 1.0
HE1 A:HIS305 3.2 5.8 1.0
HE1 A:HIS303 3.2 7.8 1.0
HD2 A:HIS305 3.3 6.2 1.0
HD2 A:HIS303 3.3 7.3 1.0
CB A:ASP238 4.0 5.6 1.0
O A:HOH778 4.0 8.1 1.0
HG3 A:LYS239 4.1 8.7 1.0
ND1 A:HIS305 4.2 5.1 1.0
ND1 A:HIS303 4.2 6.7 1.0
O A:HOH558 4.2 10.1 1.0
CG A:HIS305 4.2 5.0 1.0
CG A:HIS303 4.2 5.7 1.0
H A:ASP238 4.3 6.0 1.0
O A:HOH667 4.3 16.5 1.0
HB2 A:ASP238 4.4 6.7 1.0
HB3 A:ASP238 4.4 6.7 1.0
HE2 A:LYS239 4.6 11.8 1.0
O A:HOH666 4.7 24.4 1.0
CA A:ASP238 4.8 5.0 1.0
C A:ASP238 4.9 5.3 1.0
HD1 A:HIS305 4.9 6.1 1.0
N A:ASP238 4.9 5.0 1.0
HD1 A:HIS303 4.9 8.0 1.0

Cobalt binding site 2 out of 6 in 5esr

Go back to Cobalt Binding Sites List in 5esr
Cobalt binding site 2 out of 6 in the Crystal Structure of Haloalkane Dehalogenase (Dcca) From Caulobacter Crescentus


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 Haloalkane Dehalogenase (Dcca) From Caulobacter Crescentus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Co402

b:7.4
occ:1.00
 NE2 A:HIS306 2.1 7.0 1.0
NE2 A:HIS304 2.1 7.3 1.0
O A:HOH753 2.1 9.3 1.0
O A:HOH775 2.1 11.0 1.0
O A:HOH742 2.2 12.6 1.0
CE1 A:HIS306 3.0 7.5 1.0
CE1 A:HIS304 3.1 9.4 1.0
CD2 A:HIS304 3.1 6.4 1.0
CD2 A:HIS306 3.1 6.8 1.0
HE1 A:HIS306 3.2 9.0 1.0
HE1 A:HIS304 3.2 11.3 1.0
HD2 A:HIS304 3.3 7.7 1.0
HD2 A:HIS306 3.3 8.1 1.0
ND1 A:HIS304 4.2 8.6 1.0
ND1 A:HIS306 4.2 8.0 1.0
O A:HOH872 4.2 20.8 1.0
O A:HOH833 4.2 29.2 1.0
CG A:HIS304 4.2 7.2 1.0
CG A:HIS306 4.2 6.7 1.0
O A:HOH886 4.6 48.7 1.0
HD1 A:HIS306 4.9 9.6 1.0
HD1 A:HIS304 4.9 10.3 1.0

Cobalt binding site 3 out of 6 in 5esr

Go back to Cobalt Binding Sites List in 5esr
Cobalt binding site 3 out of 6 in the Crystal Structure of Haloalkane Dehalogenase (Dcca) From Caulobacter Crescentus


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 Haloalkane Dehalogenase (Dcca) From Caulobacter Crescentus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Co403

b:9.1
occ:1.00
 O A:HOH782 2.2 16.3 1.0
O A:HOH809 2.3 29.8 1.0
O A:HOH797 2.4 24.1 1.0
OE2 A:GLU25 2.4 18.8 1.0
OE1 A:GLU25 2.4 18.3 1.0
CD A:GLU25 2.7 16.6 1.0
O A:HOH814 4.1 26.7 1.0
CG A:GLU25 4.3 12.3 1.0
O A:HOH825 4.4 40.8 1.0
O A:HOH743 4.6 27.5 1.0
O A:HOH536 4.6 22.9 1.0
HG3 A:GLU25 4.6 14.8 1.0
HG2 A:GLU25 4.7 14.8 1.0
O A:HOH786 4.7 33.5 1.0
HB2 A:GLU25 5.0 9.7 1.0

Cobalt binding site 4 out of 6 in 5esr

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Cobalt binding site 4 out of 6 in the Crystal Structure of Haloalkane Dehalogenase (Dcca) From Caulobacter Crescentus


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 Haloalkane Dehalogenase (Dcca) From Caulobacter Crescentus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Co405

b:13.0
occ:0.50
 O A:HOH537 1.8 16.7 1.0
O A:HOH630 2.0 14.7 1.0
OE2 A:GLU256 2.1 23.8 1.0
OE1 A:GLU256 2.2 25.5 1.0
O A:HOH562 2.3 11.2 1.0
CD A:GLU256 2.5 24.5 1.0
O A:HOH851 2.8 41.9 1.0
HG1 A:THR273 3.3 18.8 1.0
HB2 A:PHE245 3.6 7.8 1.0
HG1 A:THR243 3.7 13.5 1.0
CG A:GLU256 4.0 12.3 1.0
OG1 A:THR273 4.0 15.6 1.0
OG1 A:THR243 4.1 11.2 1.0
H A:PHE245 4.1 8.1 1.0
O A:THR272 4.2 11.6 1.0
O A:HOH696 4.3 14.4 1.0
HG3 A:GLU256 4.3 14.8 1.0
O A:HOH522 4.3 20.4 1.0
HG2 A:GLU256 4.4 14.8 1.0
CB A:PHE245 4.6 6.5 1.0
HB A:THR243 4.6 10.4 1.0
HA A:THR273 4.6 10.2 1.0
HB3 A:HIS271 4.6 17.2 1.0
HD11 A:LEU260 4.7 19.0 1.0
HB2 A:GLU256 4.8 15.2 1.0
C A:THR272 4.8 10.8 1.0
HB3 A:GLU256 4.8 15.2 1.0
CB A:GLU256 4.8 12.6 1.0
N A:PHE245 4.8 6.8 1.0
HD1 A:PHE245 4.9 9.0 1.0
CB A:THR243 4.9 8.7 1.0

Cobalt binding site 5 out of 6 in 5esr

Go back to Cobalt Binding Sites List in 5esr
Cobalt binding site 5 out of 6 in the Crystal Structure of Haloalkane Dehalogenase (Dcca) From Caulobacter Crescentus


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 5 of Crystal Structure of Haloalkane Dehalogenase (Dcca) From Caulobacter Crescentus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Co406

b:10.9
occ:0.54
 OD1 A:ASP123 2.1 14.5 1.0
O A:HOH803 2.4 28.4 1.0
CL A:CL409 2.4 19.9 1.0
O A:HOH747 2.5 33.5 1.0
CG A:ASP123 2.8 10.3 1.0
OD2 A:ASP123 2.8 8.4 1.0
HD1 A:TRP124 3.3 8.8 1.0
HB3 A:GLU55 3.4 8.2 1.0
HE1 A:PHE160 3.5 12.5 1.0
CD1 A:TRP124 3.9 7.3 1.0
HE1 A:TRP163 3.9 13.8 1.0
HE1 A:TRP124 4.0 8.1 1.0
HG2 A:GLU55 4.1 8.1 1.0
HE1 A:HIS278 4.2 10.0 1.0
NE1 A:TRP124 4.2 6.8 1.0
CB A:GLU55 4.3 6.8 1.0
CB A:ASP123 4.3 8.5 1.0
O A:HOH838 4.3 33.0 1.0
O A:HOH824 4.3 36.9 1.0
H A:TRP124 4.4 6.6 1.0
HG21 A:VAL215 4.4 8.8 1.0
CE1 A:PHE160 4.4 10.4 1.0
H A:GLU55 4.4 7.6 1.0
HD1 A:PHE160 4.4 11.9 1.0
NE1 A:TRP163 4.5 11.5 1.0
HB2 A:ASP123 4.6 10.2 1.0
CG A:GLU55 4.6 6.7 1.0
HA A:ASP123 4.6 10.3 1.0
HB2 A:GLU55 4.6 8.2 1.0
CE1 A:HIS278 4.7 8.4 1.0
HG3 A:GLU55 4.7 8.1 1.0
HD1 A:TRP163 4.7 12.9 1.0
NE2 A:HIS278 4.8 9.6 1.0
HG21 A:ILE251 4.8 21.3 1.0
O A:HOH564 4.8 8.9 1.0
CD1 A:PHE160 4.8 9.9 1.0
HB3 A:ASP123 4.8 10.2 1.0
N A:TRP124 4.9 5.5 1.0
CD1 A:TRP163 4.9 10.8 1.0
CA A:ASP123 4.9 8.6 1.0
CG A:TRP124 5.0 6.1 1.0

Cobalt binding site 6 out of 6 in 5esr

Go back to Cobalt Binding Sites List in 5esr
Cobalt binding site 6 out of 6 in the Crystal Structure of Haloalkane Dehalogenase (Dcca) From Caulobacter Crescentus


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 6 of Crystal Structure of Haloalkane Dehalogenase (Dcca) From Caulobacter Crescentus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Co407

b:9.1
occ:0.55
 O A:HOH768 1.9 37.9 1.0
NE2 A:HIS22 2.2 23.7 1.0
O A:HOH766 2.2 23.6 1.0
O A:ASP40 2.3 11.1 1.0
O A:HOH674 2.3 23.7 1.0
HE1 A:HIS22 2.6 24.1 1.0
O A:HOH542 2.7 11.3 1.0
CE1 A:HIS22 2.7 20.1 1.0
O A:HOH813 3.2 9.1 1.0
HB3 A:ASP40 3.2 12.1 1.0
H A:ASP40 3.2 8.0 1.0
C A:ASP40 3.4 9.8 1.0
CD2 A:HIS22 3.4 13.9 1.0
HD2 A:HIS22 3.8 16.7 1.0
OE2 A:GLU41 3.9 19.0 1.0
HB3 A:ALA20 3.9 20.1 1.0
N A:ASP40 3.9 6.7 1.0
ND1 A:HIS22 4.0 25.0 1.0
CA A:ASP40 4.0 7.5 1.0
CB A:ASP40 4.0 10.1 1.0
HA A:GLU41 4.2 12.1 1.0
CG A:HIS22 4.3 15.5 1.0
O A:ALA20 4.5 9.7 1.0
CD A:GLU41 4.5 16.8 1.0
N A:GLU41 4.5 9.0 1.0
O A:HOH758 4.6 30.8 1.0
HB2 A:ASP40 4.6 12.1 1.0
HD1 A:HIS22 4.7 30.0 1.0
O A:HOH568 4.7 19.0 1.0
O A:HOH783 4.8 38.3 1.0
HG2 A:GLU41 4.8 16.4 1.0
O A:HOH735 4.8 33.9 1.0
CA A:GLU41 4.8 10.1 1.0
HA A:VAL39 4.9 8.3 1.0
HZ3 A:LYS44 4.9 42.8 1.0
CB A:ALA20 4.9 16.8 1.0
H A:ALA20 4.9 13.2 1.0
HA A:ASP40 5.0 9.0 1.0
CG A:ASP40 5.0 13.5 1.0

Reference:

L.Carlucci, E.Zhou, V.N.Malashkevich, S.C.Almo, E.C.Mundorff. Biochemical Characterization of Two Haloalkane Dehalogenases: Dcca From Caulobacter Crescentus and Dsaa From Saccharomonospora Azurea. Protein Sci. V. 25 877 2016.
ISSN: ESSN 1469-896X
PubMed: 26833751
DOI: 10.1002/PRO.2895
Page generated: Sun Dec 13 10:47:16 2020

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