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Cobalt in PDB 5w3w: Crystal Structure of Ssopox ASD6 Mutant (V27A-Y97W-L228M-W263M) - Open Form

Enzymatic activity of Crystal Structure of Ssopox ASD6 Mutant (V27A-Y97W-L228M-W263M) - Open Form

All present enzymatic activity of Crystal Structure of Ssopox ASD6 Mutant (V27A-Y97W-L228M-W263M) - Open Form:
3.1.8.1;

Protein crystallography data

The structure of Crystal Structure of Ssopox ASD6 Mutant (V27A-Y97W-L228M-W263M) - Open Form, PDB code: 5w3w was solved by J.Hiblot, G.Gotthard, P.Jacquet, D.Daude, C.Bergonzi, E.Chabriere, M.Elias, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.67 / 2.95
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 82.340, 105.010, 153.150, 90.00, 90.00, 90.00
R / Rfree (%) 22.9 / 28.8

Other elements in 5w3w:

The structure of Crystal Structure of Ssopox ASD6 Mutant (V27A-Y97W-L228M-W263M) - Open Form also contains other interesting chemical elements:

Iron (Fe) 4 atoms

Cobalt Binding Sites:

The binding sites of Cobalt atom in the Crystal Structure of Ssopox ASD6 Mutant (V27A-Y97W-L228M-W263M) - Open Form (pdb code 5w3w). 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 Ssopox ASD6 Mutant (V27A-Y97W-L228M-W263M) - Open Form, PDB code: 5w3w:
Jump to Cobalt binding site number: 1; 2; 3; 4;

Cobalt binding site 1 out of 4 in 5w3w

Go back to Cobalt Binding Sites List in 5w3w
Cobalt binding site 1 out of 4 in the Crystal Structure of Ssopox ASD6 Mutant (V27A-Y97W-L228M-W263M) - Open Form


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 Ssopox ASD6 Mutant (V27A-Y97W-L228M-W263M) - Open Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Co402

b:13.8
occ:1.00
 OQ1 A:KCX137 1.9 47.0 1.0
NE2 A:HIS199 2.0 56.5 1.0
ND1 A:HIS170 2.1 52.0 1.0
O A:HOH508 2.5 18.3 1.0
CX A:KCX137 2.8 49.5 1.0
CE1 A:HIS199 2.8 50.8 1.0
CD2 A:HIS199 3.0 58.5 1.0
CE1 A:HIS170 3.1 55.5 1.0
CG A:HIS170 3.1 53.5 1.0
OQ2 A:KCX137 3.1 46.5 1.0
FE A:FE401 3.2 13.8 1.0
CB A:HIS170 3.4 54.8 1.0
NH2 A:ARG223 3.7 54.5 1.0
OD2 A:ASP256 3.8 51.8 1.0
ND1 A:HIS199 4.0 50.7 1.0
NE2 A:HIS22 4.0 57.2 1.0
NZ A:KCX137 4.0 53.3 1.0
CE1 A:HIS22 4.1 55.4 1.0
CG A:HIS199 4.1 56.5 1.0
NE2 A:HIS170 4.2 55.1 1.0
CD2 A:HIS170 4.2 53.8 1.0
NE1 A:TRP97 4.3 58.7 1.0
CA A:HIS170 4.3 58.7 1.0
OD1 A:ASP256 4.5 55.4 1.0
CG A:ASP256 4.6 53.3 1.0
CE A:KCX137 4.6 53.5 1.0
CZ A:ARG223 4.6 59.1 1.0
NE A:ARG223 4.8 61.1 1.0

Cobalt binding site 2 out of 4 in 5w3w

Go back to Cobalt Binding Sites List in 5w3w
Cobalt binding site 2 out of 4 in the Crystal Structure of Ssopox ASD6 Mutant (V27A-Y97W-L228M-W263M) - Open Form


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 Ssopox ASD6 Mutant (V27A-Y97W-L228M-W263M) - Open Form within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Co402

b:49.3
occ:1.00
 OQ2 B:KCX137 1.9 70.5 1.0
ND1 B:HIS170 2.0 93.6 1.0
NE2 B:HIS199 2.0 87.9 1.0
O B:HOH503 2.0 37.3 1.0
CE1 B:HIS170 2.9 99.0 1.0
CE1 B:HIS199 2.9 85.9 1.0
CD2 B:HIS199 3.0 88.6 1.0
CX B:KCX137 3.1 62.6 1.0
CG B:HIS170 3.1 92.4 1.0
FE B:FE401 3.3 44.6 1.0
OQ1 B:KCX137 3.4 59.2 1.0
CB B:HIS170 3.5 88.2 1.0
NH2 B:ARG223 3.6 0.0 1.0
OD2 B:ASP256 3.9 95.4 1.0
ND1 B:HIS199 4.0 86.0 1.0
NE2 B:HIS170 4.0 96.3 1.0
NE2 B:HIS22 4.1 79.9 1.0
CG B:HIS199 4.1 89.0 1.0
CE1 B:HIS22 4.1 73.8 1.0
CD2 B:HIS170 4.1 96.1 1.0
NZ B:KCX137 4.2 59.5 1.0
NE1 B:TRP97 4.2 90.8 1.0
OD1 B:ASP256 4.4 92.8 1.0
CA B:HIS170 4.4 90.8 1.0
CZ B:ARG223 4.4 0.3 1.0
CG B:ASP256 4.5 98.3 1.0
NE B:ARG223 4.7 0.8 1.0
CE B:KCX137 4.7 57.5 1.0
CZ2 B:TRP97 4.8 94.1 1.0
CE2 B:TRP97 4.9 90.0 1.0

Cobalt binding site 3 out of 4 in 5w3w

Go back to Cobalt Binding Sites List in 5w3w
Cobalt binding site 3 out of 4 in the Crystal Structure of Ssopox ASD6 Mutant (V27A-Y97W-L228M-W263M) - Open Form


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 Ssopox ASD6 Mutant (V27A-Y97W-L228M-W263M) - Open Form within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Co402

b:66.5
occ:1.00
 OQ1 C:KCX137 1.9 0.9 1.0
NE2 C:HIS199 1.9 0.3 1.0
O C:HOH502 2.0 53.7 1.0
ND1 C:HIS170 2.1 0.6 1.0
CE1 C:HIS199 2.8 0.4 1.0
CX C:KCX137 2.8 0.6 1.0
CD2 C:HIS199 2.9 1.0 1.0
CG C:HIS170 3.0 0.9 1.0
CE1 C:HIS170 3.1 0.0 1.0
OQ2 C:KCX137 3.1 95.6 1.0
CB C:HIS170 3.3 0.5 1.0
FE C:FE401 3.4 50.8 1.0
NH2 C:ARG223 3.8 0.8 1.0
ND1 C:HIS199 3.9 0.0 1.0
CG C:HIS199 4.0 0.1 1.0
NZ C:KCX137 4.0 0.6 1.0
NE2 C:HIS22 4.0 0.6 1.0
CE1 C:HIS22 4.1 0.9 1.0
NE2 C:HIS170 4.2 0.3 1.0
CD2 C:HIS170 4.2 0.7 1.0
CA C:HIS170 4.2 0.5 1.0
OD2 C:ASP256 4.4 0.2 1.0
OD1 C:ASP256 4.5 0.3 1.0
NE1 C:TRP97 4.5 93.8 1.0
CE C:KCX137 4.5 0.7 1.0
CZ C:ARG223 4.7 0.1 1.0
CZ2 C:TRP97 4.7 93.1 1.0
CG C:ASP256 4.7 0.1 1.0
NE C:ARG223 4.9 0.2 1.0
CE2 C:TRP97 5.0 91.8 1.0

Cobalt binding site 4 out of 4 in 5w3w

Go back to Cobalt Binding Sites List in 5w3w
Cobalt binding site 4 out of 4 in the Crystal Structure of Ssopox ASD6 Mutant (V27A-Y97W-L228M-W263M) - Open Form


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 Ssopox ASD6 Mutant (V27A-Y97W-L228M-W263M) - Open Form within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Co402

b:28.3
occ:1.00
 O D:HOH503 1.9 23.5 1.0
OQ2 D:KCX137 1.9 52.1 1.0
NE2 D:HIS199 1.9 66.5 1.0
ND1 D:HIS170 2.0 63.7 1.0
CE1 D:HIS199 2.8 68.3 1.0
CD2 D:HIS199 2.9 67.7 1.0
CE1 D:HIS170 2.9 64.2 1.0
CX D:KCX137 2.9 47.6 1.0
CG D:HIS170 3.1 56.6 1.0
OQ1 D:KCX137 3.2 45.0 1.0
FE D:FE401 3.4 19.7 1.0
CB D:HIS170 3.5 54.1 1.0
NH2 D:ARG223 3.6 76.9 1.0
OD2 D:ASP256 3.9 69.2 1.0
ND1 D:HIS199 3.9 70.7 1.0
CG D:HIS199 4.0 67.9 1.0
NE2 D:HIS170 4.0 57.9 1.0
NE2 D:HIS22 4.1 53.1 1.0
CE1 D:HIS22 4.1 52.9 1.0
CD2 D:HIS170 4.1 55.4 1.0
NZ D:KCX137 4.1 46.2 1.0
CA D:HIS170 4.3 53.3 1.0
CZ D:ARG223 4.4 79.2 1.0
NE1 D:TRP97 4.5 65.6 1.0
OD1 D:ASP256 4.5 67.8 1.0
O3 D:GOL407 4.5 58.4 1.0
CG D:ASP256 4.5 71.1 1.0
CE D:KCX137 4.6 48.5 1.0
O2 D:GOL407 4.7 65.7 1.0
NE D:ARG223 4.7 79.2 1.0

Reference:

P.Jacquet, J.Hiblot, D.Daude, C.Bergonzi, G.Gotthard, N.Armstrong, E.Chabriere, M.Elias. Rational Engineering of A Native Hyperthermostable Lactonase Into A Broad Spectrum Phosphotriesterase. Sci Rep V. 7 16745 2017.
ISSN: ESSN 2045-2322
PubMed: 29196634
DOI: 10.1038/S41598-017-16841-0
Page generated: Tue Jul 30 18:18:07 2024

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