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Cobalt in PDB 2qb7: Saccharomyces Cerevisiae Cytosolic Exopolyphosphatase, Phosphate Complex

Enzymatic activity of Saccharomyces Cerevisiae Cytosolic Exopolyphosphatase, Phosphate Complex

All present enzymatic activity of Saccharomyces Cerevisiae Cytosolic Exopolyphosphatase, Phosphate Complex:
3.6.1.11;

Protein crystallography data

The structure of Saccharomyces Cerevisiae Cytosolic Exopolyphosphatase, Phosphate Complex, PDB code: 2qb7 was solved by S.A.White, E.Ugochukwu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 67.42 / 1.60
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 79.992, 83.039, 118.900, 90.00, 90.00, 90.00
R / Rfree (%) 17.1 / 20.1

Cobalt Binding Sites:

The binding sites of Cobalt atom in the Saccharomyces Cerevisiae Cytosolic Exopolyphosphatase, Phosphate Complex (pdb code 2qb7). This binding sites where shown within 5.0 Angstroms radius around Cobalt atom.
In total 4 binding sites of Cobalt where determined in the Saccharomyces Cerevisiae Cytosolic Exopolyphosphatase, Phosphate Complex, PDB code: 2qb7:
Jump to Cobalt binding site number: 1; 2; 3; 4;

Cobalt binding site 1 out of 4 in 2qb7

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Cobalt binding site 1 out of 4 in the Saccharomyces Cerevisiae Cytosolic Exopolyphosphatase, Phosphate Complex


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 1 of Saccharomyces Cerevisiae Cytosolic Exopolyphosphatase, Phosphate Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Co401

b:10.6
occ:1.00
O2 A:PO4501 2.0 13.3 1.0
OD2 A:ASP41 2.1 10.5 1.0
OD1 A:ASP127 2.1 9.3 1.0
NE2 A:HIS148 2.2 11.8 1.0
O A:HOH1354 2.2 15.0 1.0
CG A:ASP127 2.9 10.3 1.0
OD2 A:ASP127 3.0 10.5 1.0
CE1 A:HIS148 3.1 10.8 1.0
CG A:ASP41 3.1 10.0 1.0
CD2 A:HIS148 3.3 9.3 1.0
P A:PO4501 3.3 14.1 1.0
CB A:ASP41 3.5 9.2 1.0
O1 A:PO4501 3.7 14.9 1.0
O A:HOH1293 3.9 21.9 1.0
CE1 A:HIS149 3.9 10.8 1.0
O3 A:PO4501 4.1 15.0 1.0
CB A:CYS169 4.2 11.2 1.0
N A:CYS169 4.2 11.5 1.0
OD1 A:ASP41 4.2 10.7 1.0
ND1 A:HIS148 4.2 10.2 1.0
O A:HOH1292 4.3 18.2 1.0
CB A:ASP127 4.3 9.7 1.0
O4 A:PO4501 4.3 16.3 1.0
CG A:HIS148 4.4 9.6 1.0
NE2 A:HIS149 4.4 11.1 1.0
OD2 A:ASP202 4.4 14.3 1.0
OD2 A:ASP39 4.7 12.2 1.0
CA A:CYS169 4.8 11.6 1.0
CA A:ASP127 4.9 10.7 1.0
ND1 A:HIS149 4.9 10.8 1.0
CA A:ASP41 4.9 9.7 1.0

Cobalt binding site 2 out of 4 in 2qb7

Go back to Cobalt Binding Sites List in 2qb7
Cobalt binding site 2 out of 4 in the Saccharomyces Cerevisiae Cytosolic Exopolyphosphatase, Phosphate Complex


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 2 of Saccharomyces Cerevisiae Cytosolic Exopolyphosphatase, Phosphate Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Co402

b:11.8
occ:1.00
O2 A:PO4503 2.0 12.8 1.0
O3 A:PO4501 2.1 15.0 1.0
O A:HOH1309 2.2 11.5 1.0
O A:HOH1355 2.2 13.6 1.0
O A:HOH1010 2.2 11.3 1.0
O A:HOH979 2.2 11.2 1.0
P A:PO4501 3.3 14.1 1.0
P A:PO4503 3.3 13.7 1.0
O4 A:PO4503 3.7 14.3 1.0
O1 A:PO4501 3.8 14.9 1.0
OD2 A:ASP39 3.8 12.2 1.0
O4 A:PO4501 3.8 16.3 1.0
O A:HOH1292 3.9 18.2 1.0
NH2 A:ARG381 4.0 11.9 1.0
O3 A:PO4503 4.1 14.4 1.0
O A:HOH929 4.1 13.6 1.0
O4 A:PO4502 4.1 21.8 1.0
O1 A:PO4502 4.1 17.8 1.0
O A:HOH917 4.2 12.4 1.0
OD2 A:ASP266 4.3 11.8 1.0
O A:HOH1140 4.3 22.0 1.0
O A:HOH1017 4.3 14.8 1.0
OD1 A:ASP266 4.4 10.8 1.0
O1 A:PO4503 4.5 13.1 1.0
O2 A:PO4501 4.6 13.3 1.0
P A:PO4502 4.7 19.8 1.0
CG A:ASP266 4.8 9.4 1.0
CG A:ASP39 4.8 12.3 1.0
OG A:SER37 4.9 13.0 1.0

Cobalt binding site 3 out of 4 in 2qb7

Go back to Cobalt Binding Sites List in 2qb7
Cobalt binding site 3 out of 4 in the Saccharomyces Cerevisiae Cytosolic Exopolyphosphatase, Phosphate Complex


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 3 of Saccharomyces Cerevisiae Cytosolic Exopolyphosphatase, Phosphate Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Co401

b:14.6
occ:1.00
OD2 B:ASP41 2.1 13.5 1.0
OD1 B:ASP127 2.1 13.1 1.0
O2 B:PO4501 2.1 19.9 1.0
NE2 B:HIS148 2.2 15.5 1.0
O B:HOH1219 2.2 16.1 1.0
CG B:ASP127 2.9 13.0 1.0
CE1 B:HIS148 3.0 14.8 1.0
OD2 B:ASP127 3.0 13.1 1.0
CG B:ASP41 3.1 14.0 1.0
CD2 B:HIS148 3.3 15.7 1.0
P B:PO4501 3.4 21.4 1.0
CB B:ASP41 3.6 13.6 1.0
O3 B:PO4501 3.8 20.8 1.0
CE1 B:HIS149 3.9 17.3 1.0
O B:HOH1163 3.9 26.6 1.0
ND1 B:HIS148 4.2 14.7 1.0
CB B:CYS169 4.2 14.1 1.0
OD1 B:ASP41 4.2 15.0 1.0
N B:CYS169 4.2 13.9 1.0
O4 B:PO4501 4.2 17.7 1.0
O B:HOH1161 4.3 23.5 1.0
CB B:ASP127 4.3 13.5 1.0
CG B:HIS148 4.3 15.5 1.0
OD2 B:ASP202 4.4 15.7 1.0
O1 B:PO4501 4.4 20.8 1.0
NE2 B:HIS149 4.4 17.6 1.0
OD2 B:ASP39 4.7 17.6 1.0
CA B:ASP127 4.9 14.0 1.0
ND1 B:HIS149 4.9 16.2 1.0
CA B:CYS169 4.9 14.1 1.0
CA B:ASP41 5.0 13.6 1.0

Cobalt binding site 4 out of 4 in 2qb7

Go back to Cobalt Binding Sites List in 2qb7
Cobalt binding site 4 out of 4 in the Saccharomyces Cerevisiae Cytosolic Exopolyphosphatase, Phosphate Complex


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 4 of Saccharomyces Cerevisiae Cytosolic Exopolyphosphatase, Phosphate Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Co402

b:19.1
occ:1.00
O2 B:PO4502 2.1 19.8 1.0
O4 B:PO4501 2.1 17.7 1.0
O B:HOH1220 2.2 22.4 1.0
O B:HOH1183 2.2 17.5 1.0
O B:HOH953 2.2 14.2 1.0
O B:HOH973 2.3 19.2 1.0
P B:PO4501 3.3 21.4 1.0
P B:PO4502 3.4 19.7 1.0
O3 B:PO4502 3.8 20.3 1.0
O3 B:PO4501 3.8 20.8 1.0
O1 B:PO4501 3.8 20.8 1.0
OD2 B:ASP39 3.9 17.6 1.0
O B:HOH1161 3.9 23.5 1.0
O4 B:PO4503 4.1 28.3 1.0
O1 B:PO4502 4.1 19.4 1.0
O B:HOH962 4.1 21.0 1.0
O1 B:PO4503 4.1 28.9 1.0
NH2 B:ARG381 4.1 19.0 1.0
O B:HOH919 4.1 18.6 1.0
OD2 B:ASP266 4.3 19.3 1.0
O B:HOH1188 4.3 40.8 1.0
OD1 B:ASP266 4.4 17.0 1.0
O B:HOH1081 4.4 19.4 1.0
O4 B:PO4502 4.5 19.4 1.0
O2 B:PO4501 4.5 19.9 1.0
P B:PO4503 4.7 28.5 1.0
CG B:ASP266 4.8 18.3 1.0
CG B:ASP39 4.8 17.1 1.0
OG B:SER37 5.0 18.2 1.0

Reference:

E.Ugochukwu, A.L.Lovering, O.C.Mather, T.W.Young, S.A.White. The Crystal Structure of the Cytosolic Exopolyphosphatase From Saccharomyces Cerevisiae Reveals the Basis For Substrate Specificity. J.Mol.Biol. V. 371 1007 2007.
ISSN: ISSN 0022-2836
PubMed: 17599355
DOI: 10.1016/J.JMB.2007.05.066
Page generated: Sun Dec 13 10:38:47 2020

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