Iodine in PDB 3onn: Crystal Structure of 5'-Nucleotidase SDT1 From Saccharomyces Cerevisiae

Protein crystallography data

The structure of Crystal Structure of 5'-Nucleotidase SDT1 From Saccharomyces Cerevisiae, PDB code: 3onn was solved by M.K.Teng, L.W.Niu, N.Shi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 38.77 / 1.87
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 40.720, 77.550, 82.160, 90.00, 90.00, 90.00
R / Rfree (%) 19.8 / 25

Other elements in 3onn:

The structure of Crystal Structure of 5'-Nucleotidase SDT1 From Saccharomyces Cerevisiae also contains other interesting chemical elements:

Magnesium (Mg) 1 atom

Iodine Binding Sites:

The binding sites of Iodine atom in the Crystal Structure of 5'-Nucleotidase SDT1 From Saccharomyces Cerevisiae (pdb code 3onn). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 4 binding sites of Iodine where determined in the Crystal Structure of 5'-Nucleotidase SDT1 From Saccharomyces Cerevisiae, PDB code: 3onn:
Jump to Iodine binding site number: 1; 2; 3; 4;

Iodine binding site 1 out of 4 in 3onn

Go back to Iodine Binding Sites List in 3onn
Iodine binding site 1 out of 4 in the Crystal Structure of 5'-Nucleotidase SDT1 From Saccharomyces Cerevisiae


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 1 of Crystal Structure of 5'-Nucleotidase SDT1 From Saccharomyces Cerevisiae within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I272

b:26.8
occ:0.85
N A:ASN96 3.7 16.7 1.0
CZ A:PHE59 4.2 15.2 1.0
CD2 A:HIS63 4.2 22.9 1.0
CG1 A:VAL95 4.2 16.4 1.0
CG A:GLU99 4.3 22.0 1.0
CB A:ASN96 4.4 18.1 1.0
CA A:VAL95 4.4 16.2 1.0
O A:ASN96 4.4 14.3 1.0
CA A:ASN96 4.6 18.1 1.0
CB A:GLU99 4.6 19.1 1.0
C A:VAL95 4.6 16.7 1.0
CE1 A:PHE59 4.6 16.6 1.0
CB A:VAL95 4.7 13.9 1.0
CG2 A:VAL95 4.7 14.7 1.0
NE2 A:HIS63 4.9 24.1 1.0
C A:ASN96 5.0 14.3 1.0

Iodine binding site 2 out of 4 in 3onn

Go back to Iodine Binding Sites List in 3onn
Iodine binding site 2 out of 4 in the Crystal Structure of 5'-Nucleotidase SDT1 From Saccharomyces Cerevisiae


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 2 of Crystal Structure of 5'-Nucleotidase SDT1 From Saccharomyces Cerevisiae within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I273

b:35.4
occ:0.53
O A:HOH415 2.9 36.7 1.0
NE A:ARG149 3.3 28.0 1.0
CB A:GLN111 3.5 27.0 1.0
NE2 A:GLN111 3.7 27.5 1.0
CD2 A:LEU3 3.7 25.7 1.0
NH1 A:ARG149 3.7 27.3 1.0
CG A:LEU3 3.9 26.3 1.0
CZ A:ARG149 4.0 29.0 1.0
CD A:ARG149 4.4 24.2 1.0
CA A:GLN111 4.4 26.0 1.0
CG A:GLN111 4.4 33.5 1.0
CD A:GLN111 4.4 35.4 1.0
N A:GLN111 4.4 23.4 1.0
CG A:ARG149 4.5 23.4 1.0
CD1 A:LEU153 4.5 14.5 1.0
CD2 A:LEU153 4.6 15.4 1.0
N A:LEU3 4.6 31.6 1.0
CD1 A:LEU3 4.9 29.5 1.0
CG A:LEU153 4.9 15.6 1.0
CB A:LEU3 5.0 28.8 1.0
CA A:LEU3 5.0 27.1 1.0

Iodine binding site 3 out of 4 in 3onn

Go back to Iodine Binding Sites List in 3onn
Iodine binding site 3 out of 4 in the Crystal Structure of 5'-Nucleotidase SDT1 From Saccharomyces Cerevisiae


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 3 of Crystal Structure of 5'-Nucleotidase SDT1 From Saccharomyces Cerevisiae within 5.0Å range:

Iodine binding site 4 out of 4 in 3onn

Go back to Iodine Binding Sites List in 3onn
Iodine binding site 4 out of 4 in the Crystal Structure of 5'-Nucleotidase SDT1 From Saccharomyces Cerevisiae


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 4 of Crystal Structure of 5'-Nucleotidase SDT1 From Saccharomyces Cerevisiae within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I275

b:35.1
occ:0.38
O A:HOH416 2.8 33.7 1.0
N A:ASP167 3.2 16.7 1.0
NZ A:LYS185 3.2 29.0 1.0
CB A:ASP167 3.5 23.6 1.0
O A:VAL175 3.8 17.3 1.0
CA A:ASP167 3.9 19.3 1.0
CB A:VAL175 4.0 25.3 1.0
N A:VAL175 4.1 25.4 1.0
C A:CYS166 4.2 13.8 1.0
O A:ASP167 4.3 24.6 1.0
CA A:CYS166 4.3 12.4 1.0
CE A:LYS185 4.3 24.1 1.0
O A:HOH364 4.4 21.2 1.0
CA A:VAL175 4.4 23.7 1.0
O A:TYR165 4.4 15.0 1.0
C A:ASP167 4.5 18.8 1.0
C A:VAL175 4.6 21.2 1.0
SG A:CYS166 4.6 13.1 1.0
CD A:LYS185 4.7 25.4 1.0
CG1 A:VAL175 4.8 23.2 1.0
CG A:ASP167 4.8 27.2 1.0
CG2 A:VAL175 4.8 28.1 1.0

Reference:

N.Shi, M.K.Teng, L.W.Niu. Crystal Structure of the First Pyrimidine 5'-Nucleotidase SDT1 From Saccharomyces Cerevisiae To Be Published.
Page generated: Sun Dec 13 19:28:56 2020

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