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Cobalt in PDB 2pau: Crystal Structure of the 5'-Deoxynucleotidase Yfbr Mutant E72A Complexed with Co(2+) and Damp

Enzymatic activity of Crystal Structure of the 5'-Deoxynucleotidase Yfbr Mutant E72A Complexed with Co(2+) and Damp

All present enzymatic activity of Crystal Structure of the 5'-Deoxynucleotidase Yfbr Mutant E72A Complexed with Co(2+) and Damp:
3.1.3.5;

Protein crystallography data

The structure of Crystal Structure of the 5'-Deoxynucleotidase Yfbr Mutant E72A Complexed with Co(2+) and Damp, PDB code: 2pau was solved by M.D.Zimmerman, M.Proudfoot, A.Yakunin, W.Minor, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 40.13 / 2.10
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 135.595, 135.595, 54.936, 90.00, 90.00, 120.00
R / Rfree (%) 19.3 / 26

Cobalt Binding Sites:

The binding sites of Cobalt atom in the Crystal Structure of the 5'-Deoxynucleotidase Yfbr Mutant E72A Complexed with Co(2+) and Damp (pdb code 2pau). This binding sites where shown within 5.0 Angstroms radius around Cobalt atom.
In total 2 binding sites of Cobalt where determined in the Crystal Structure of the 5'-Deoxynucleotidase Yfbr Mutant E72A Complexed with Co(2+) and Damp, PDB code: 2pau:
Jump to Cobalt binding site number: 1; 2;

Cobalt binding site 1 out of 2 in 2pau

Go back to Cobalt Binding Sites List in 2pau
Cobalt binding site 1 out of 2 in the Crystal Structure of the 5'-Deoxynucleotidase Yfbr Mutant E72A Complexed with Co(2+) and Damp


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 the 5'-Deoxynucleotidase Yfbr Mutant E72A Complexed with Co(2+) and Damp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Co201

b:39.1
occ:0.70
NE2 A:HIS33 2.0 29.2 1.0
NE2 A:HIS68 2.1 36.5 1.0
OD1 A:ASP137 2.2 42.9 1.0
O A:HOH425 2.2 38.2 0.7
O1P A:D5M301 2.3 53.3 0.7
OD2 A:ASP69 2.3 36.5 1.0
CE1 A:HIS33 2.9 35.6 1.0
CD2 A:HIS68 3.1 38.2 1.0
CG A:ASP137 3.1 45.2 1.0
CE1 A:HIS68 3.1 39.2 1.0
CG A:ASP69 3.1 37.1 1.0
CD2 A:HIS33 3.1 36.1 1.0
OD1 A:ASP69 3.3 37.5 1.0
OD2 A:ASP137 3.5 49.7 1.0
P A:D5M301 3.7 57.6 0.7
ND1 A:HIS33 4.0 34.0 1.0
CG A:HIS33 4.2 35.1 1.0
CG A:HIS68 4.2 35.1 1.0
ND1 A:HIS68 4.2 32.6 1.0
NH1 A:ARG18 4.2 55.3 1.0
O2P A:D5M301 4.3 55.0 0.7
CB A:ASP137 4.4 41.4 1.0
O3P A:D5M301 4.4 54.9 0.7
CB A:ASP69 4.5 33.8 1.0
CG2 A:VAL37 4.6 37.2 1.0
O1 A:PEG401 4.6 56.6 1.0
O5' A:D5M301 4.8 52.5 0.7

Cobalt binding site 2 out of 2 in 2pau

Go back to Cobalt Binding Sites List in 2pau
Cobalt binding site 2 out of 2 in the Crystal Structure of the 5'-Deoxynucleotidase Yfbr Mutant E72A Complexed with Co(2+) and Damp


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 the 5'-Deoxynucleotidase Yfbr Mutant E72A Complexed with Co(2+) and Damp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Co201

b:40.7
occ:0.90
NE2 B:HIS33 2.0 37.9 1.0
NE2 B:HIS68 2.1 36.6 1.0
OD2 B:ASP69 2.2 40.9 1.0
OD1 B:ASP137 2.3 45.0 1.0
O1P B:D5M301 2.4 49.2 0.9
CE1 B:HIS33 3.0 39.1 1.0
CD2 B:HIS33 3.0 37.1 1.0
CG B:ASP69 3.1 40.3 1.0
CD2 B:HIS68 3.1 39.0 1.0
CE1 B:HIS68 3.1 36.6 1.0
CG B:ASP137 3.2 43.8 1.0
OD1 B:ASP69 3.3 40.3 1.0
P B:D5M301 3.7 56.3 0.9
OD2 B:ASP137 3.8 48.8 1.0
ND1 B:HIS33 4.1 36.8 1.0
CG B:HIS33 4.2 34.5 1.0
NH1 B:ARG18 4.2 50.0 1.0
ND1 B:HIS68 4.2 38.0 1.0
CG B:HIS68 4.2 38.3 1.0
O2P B:D5M301 4.2 53.0 0.9
O3P B:D5M301 4.2 54.9 0.9
CB B:ASP137 4.4 40.5 1.0
CB B:ASP69 4.4 35.4 1.0
CG2 B:VAL37 4.6 37.8 1.0
NH2 B:ARG18 4.7 52.8 1.0
CZ B:ARG18 4.7 51.2 1.0

Reference:

M.D.Zimmerman, M.Proudfoot, A.Yakunin, W.Minor. Structural Insight Into the Mechanism of Substrate Specificity and Catalytic Activity of An Hd-Domain Phosphohydrolase: the 5'-Deoxyribonucleotidase Yfbr From Escherichia Coli. J.Mol.Biol. V. 378 215 2008.
ISSN: ISSN 0022-2836
PubMed: 18353368
DOI: 10.1016/J.JMB.2008.02.036
Page generated: Sun Dec 13 10:38:37 2020

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