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Cobalt in PDB 6zpb: Cyanophage S-2L Hd Phosphohydrolase (Datz) Bound to Da and Two Catalytic CO2+ Ions

Protein crystallography data

The structure of Cyanophage S-2L Hd Phosphohydrolase (Datz) Bound to Da and Two Catalytic CO2+ Ions, PDB code: 6zpb was solved by D.Czernecki, P.Legrand, M.Delarue, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 40.44 / 1.72
Space group H 3 2
Cell size a, b, c (Å), α, β, γ (°) 141.827, 141.827, 53.725, 90, 90, 120
R / Rfree (%) 14.6 / 17

Cobalt Binding Sites:

The binding sites of Cobalt atom in the Cyanophage S-2L Hd Phosphohydrolase (Datz) Bound to Da and Two Catalytic CO2+ Ions (pdb code 6zpb). This binding sites where shown within 5.0 Angstroms radius around Cobalt atom.
In total 3 binding sites of Cobalt where determined in the Cyanophage S-2L Hd Phosphohydrolase (Datz) Bound to Da and Two Catalytic CO2+ Ions, PDB code: 6zpb:
Jump to Cobalt binding site number: 1; 2; 3;

Cobalt binding site 1 out of 3 in 6zpb

Go back to Cobalt Binding Sites List in 6zpb
Cobalt binding site 1 out of 3 in the Cyanophage S-2L Hd Phosphohydrolase (Datz) Bound to Da and Two Catalytic CO2+ Ions


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 1 of Cyanophage S-2L Hd Phosphohydrolase (Datz) Bound to Da and Two Catalytic CO2+ Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Co202

b:11.2
occ:1.00
NE2 A:HIS34 2.1 8.3 1.0
NE2 A:HIS66 2.1 11.5 1.0
OD2 A:ASP67 2.1 9.5 1.0
OD1 A:ASP119 2.2 10.2 1.0
O A:HOH322 2.2 12.6 1.0
O A:HOH447 2.3 12.9 1.0
CE1 A:HIS34 3.1 8.5 1.0
CD2 A:HIS66 3.1 8.8 1.0
CG A:ASP67 3.1 14.1 1.0
CG A:ASP119 3.1 17.1 1.0
CE1 A:HIS66 3.2 9.1 1.0
CD2 A:HIS34 3.2 8.6 1.0
OD2 A:ASP119 3.4 14.0 1.0
OD1 A:ASP67 3.5 11.2 1.0
O A:HOH321 3.9 17.6 1.0
O A:HOH303 4.1 17.4 1.0
CG A:HIS66 4.2 11.5 1.0
O A:HOH344 4.2 16.8 1.0
ND1 A:HIS34 4.2 7.6 1.0
O A:HOH427 4.2 10.4 1.0
NH1 A:ARG19 4.2 8.9 1.0
CG A:HIS34 4.3 6.5 1.0
ND1 A:HIS66 4.3 9.5 1.0
CB A:ASP67 4.4 9.7 1.0
CB A:ASP119 4.4 10.5 1.0
O A:HOH473 4.7 26.2 1.0
CG2 A:VAL38 5.0 8.9 1.0

Cobalt binding site 2 out of 3 in 6zpb

Go back to Cobalt Binding Sites List in 6zpb
Cobalt binding site 2 out of 3 in the Cyanophage S-2L Hd Phosphohydrolase (Datz) Bound to Da and Two Catalytic CO2+ Ions


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 2 of Cyanophage S-2L Hd Phosphohydrolase (Datz) Bound to Da and Two Catalytic CO2+ Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Co203

b:12.5
occ:0.77
OD1 A:ASP75 2.0 12.1 1.0
O A:HOH321 2.0 17.6 1.0
OE2 A:GLU70 2.1 12.4 1.0
O A:HOH303 2.1 17.4 1.0
O A:HOH316 2.2 18.1 1.0
O5' A:3D1201 2.2 14.9 1.0
CG A:ASP75 3.0 15.4 1.0
CD A:GLU70 3.1 10.7 1.0
C5' A:3D1201 3.3 14.0 1.0
OE1 A:GLU70 3.3 10.2 1.0
OD2 A:ASP75 3.7 14.6 1.0
C4' A:3D1201 3.8 12.8 1.0
O A:HOH426 3.9 25.2 1.0
O A:HOH393 4.0 35.4 1.0
CB A:ASP75 4.0 10.7 1.0
O A:HOH447 4.1 12.9 1.0
OD1 A:ASP67 4.1 11.2 1.0
O A:ALA76 4.2 12.4 1.0
O A:HOH480 4.2 39.5 1.0
CA A:ASP75 4.2 9.0 1.0
O A:HOH344 4.3 16.8 1.0
C3' A:3D1201 4.4 10.3 1.0
CG A:ASP67 4.4 14.1 1.0
NH1 A:ARG19 4.4 8.9 1.0
OD2 A:ASP67 4.4 9.5 1.0
CG A:GLU70 4.4 10.3 1.0
C A:ASP75 4.6 10.0 1.0
N A:ALA76 4.7 11.3 1.0
NZ A:LYS81 4.7 26.6 1.0
O3' A:3D1201 4.8 10.6 1.0
O A:HOH322 4.9 12.6 1.0
O A:HOH498 5.0 30.1 1.0

Cobalt binding site 3 out of 3 in 6zpb

Go back to Cobalt Binding Sites List in 6zpb
Cobalt binding site 3 out of 3 in the Cyanophage S-2L Hd Phosphohydrolase (Datz) Bound to Da and Two Catalytic CO2+ Ions


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 3 of Cyanophage S-2L Hd Phosphohydrolase (Datz) Bound to Da and Two Catalytic CO2+ Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Co204

b:21.3
occ:0.47
OE1 A:GLU163 2.3 20.4 1.0
O A:HOH319 2.6 39.2 1.0
CD A:GLU163 3.4 28.0 1.0
OE2 A:GLU163 3.9 19.6 1.0
O A:HOH508 3.9 41.1 0.5
O A:HOH359 4.4 34.1 1.0
CG A:GLU163 4.6 20.9 1.0
O A:HOH433 4.9 36.3 1.0
CB A:GLU163 4.9 14.6 1.0

Reference:

D.Czernecki, P.Legrand, M.Tekpinar, S.Rosario, P.A.Kaminski, M.Delarue. How Cyanophage S-2L Rejects Adenine and Incorporates 2-Aminoadenine to Saturate Hydrogen Bonding in Its Dna Nat Commun 2021.
ISSN: ESSN 2041-1723
Page generated: Sat Apr 3 14:48:43 2021

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