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

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

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

Protein crystallography data

The structure of Crystal Structure of the 5'-Deoxynucleotidase Yfbr Mutant E72A Complexed with Co(2+) and Tmp, PDB code: 2par 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) 40.39 / 2.10
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 136.136, 136.136, 55.418, 90.00, 90.00, 120.00
R / Rfree (%) 19.4 / 24.7

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 Tmp (pdb code 2par). 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 Tmp, PDB code: 2par:
Jump to Cobalt binding site number: 1; 2;

Cobalt binding site 1 out of 2 in 2par

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


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 Tmp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Co201

b:30.2
occ:1.00
O A:HOH407 2.0 29.8 1.0
OD1 A:ASP137 2.0 26.6 1.0
NE2 A:HIS68 2.1 23.4 1.0
OD2 A:ASP69 2.2 21.2 1.0
NE2 A:HIS33 2.2 24.0 1.0
O3P A:TMP301 2.2 37.8 1.0
CD2 A:HIS68 3.1 22.7 1.0
CG A:ASP69 3.1 22.0 1.0
CG A:ASP137 3.1 26.2 1.0
CE1 A:HIS68 3.1 21.1 1.0
CD2 A:HIS33 3.1 25.2 1.0
CE1 A:HIS33 3.2 26.3 1.0
OD1 A:ASP69 3.4 22.2 1.0
P A:TMP301 3.5 44.2 1.0
OD2 A:ASP137 3.7 32.5 1.0
O1P A:TMP301 3.9 40.7 1.0
NH1 A:ARG18 4.0 26.2 1.0
O A:HOH413 4.2 34.5 1.0
ND1 A:HIS68 4.2 20.4 1.0
CG A:HIS68 4.2 21.0 1.0
O2P A:TMP301 4.2 42.9 1.0
CB A:ASP137 4.3 24.8 1.0
ND1 A:HIS33 4.3 22.3 1.0
CG A:HIS33 4.3 21.8 1.0
CB A:ASP69 4.4 22.1 1.0
O A:HOH414 4.5 39.8 1.0
O5' A:TMP301 4.7 41.5 1.0
CG2 A:VAL37 4.8 23.3 1.0
CZ A:ARG18 5.0 27.7 1.0

Cobalt binding site 2 out of 2 in 2par

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


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 Tmp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Co201

b:32.5
occ:1.00
OD1 B:ASP137 2.1 29.4 1.0
NE2 B:HIS33 2.1 27.4 1.0
NE2 B:HIS68 2.2 22.8 1.0
O1P B:TMP301 2.2 36.8 1.0
O B:HOH313 2.3 28.6 1.0
OD2 B:ASP69 2.3 28.6 1.0
CD2 B:HIS68 3.0 24.2 1.0
CG B:ASP69 3.1 26.8 1.0
CE1 B:HIS33 3.1 24.6 1.0
CD2 B:HIS33 3.1 24.6 1.0
CG B:ASP137 3.2 27.8 1.0
OD1 B:ASP69 3.2 24.2 1.0
CE1 B:HIS68 3.3 24.6 1.0
P B:TMP301 3.5 41.3 1.0
OD2 B:ASP137 3.6 28.1 1.0
O2P B:TMP301 4.0 40.1 1.0
NH1 B:ARG18 4.1 27.1 1.0
O3P B:TMP301 4.2 41.9 1.0
ND1 B:HIS33 4.2 24.7 1.0
CG B:HIS33 4.2 24.5 1.0
CG B:HIS68 4.3 23.4 1.0
ND1 B:HIS68 4.3 25.1 1.0
CB B:ASP137 4.4 25.4 1.0
CB B:ASP69 4.4 24.5 1.0
CG2 B:VAL37 4.6 21.7 1.0
CZ B:ARG18 4.8 28.9 1.0
O5' B:TMP301 4.8 39.5 1.0
NH2 B:ARG18 4.9 31.1 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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