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Sodium in PDB 4o0i: Crystal Structure of Fragment Dna Polymerase I From Bacillus Stearothermophilus with 2'-Mese-Arabino-Guanosine Derivatized Dna

Enzymatic activity of Crystal Structure of Fragment Dna Polymerase I From Bacillus Stearothermophilus with 2'-Mese-Arabino-Guanosine Derivatized Dna

All present enzymatic activity of Crystal Structure of Fragment Dna Polymerase I From Bacillus Stearothermophilus with 2'-Mese-Arabino-Guanosine Derivatized Dna:
2.7.7.7;

Protein crystallography data

The structure of Crystal Structure of Fragment Dna Polymerase I From Bacillus Stearothermophilus with 2'-Mese-Arabino-Guanosine Derivatized Dna, PDB code: 4o0i was solved by S.Jiang, J.Gan, H.Sun, Z.Huang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.04 / 2.20
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 86.770, 93.967, 106.041, 90.00, 90.00, 90.00
R / Rfree (%) 17.6 / 22.8

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Fragment Dna Polymerase I From Bacillus Stearothermophilus with 2'-Mese-Arabino-Guanosine Derivatized Dna (pdb code 4o0i). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Crystal Structure of Fragment Dna Polymerase I From Bacillus Stearothermophilus with 2'-Mese-Arabino-Guanosine Derivatized Dna, PDB code: 4o0i:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 4o0i

Go back to Sodium Binding Sites List in 4o0i
Sodium binding site 1 out of 2 in the Crystal Structure of Fragment Dna Polymerase I From Bacillus Stearothermophilus with 2'-Mese-Arabino-Guanosine Derivatized Dna


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of Fragment Dna Polymerase I From Bacillus Stearothermophilus with 2'-Mese-Arabino-Guanosine Derivatized Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na908

b:61.0
occ:1.00
OE2 A:GLU310 2.7 58.8 1.0
OG1 A:THR308 2.9 58.0 1.0
CD A:GLU310 3.5 57.0 1.0
CG2 A:THR308 3.6 51.6 1.0
CG A:GLU310 3.6 55.2 1.0
CB A:THR308 3.7 55.0 1.0
CE1 A:PHE344 4.0 41.9 1.0
CE A:MET311 4.2 43.5 1.0
OE1 A:GLU310 4.7 54.9 1.0
CZ A:PHE344 4.7 44.0 1.0
CD1 A:PHE344 4.7 35.7 1.0
O A:HOH1030 5.0 49.8 1.0

Sodium binding site 2 out of 2 in 4o0i

Go back to Sodium Binding Sites List in 4o0i
Sodium binding site 2 out of 2 in the Crystal Structure of Fragment Dna Polymerase I From Bacillus Stearothermophilus with 2'-Mese-Arabino-Guanosine Derivatized Dna


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of Fragment Dna Polymerase I From Bacillus Stearothermophilus with 2'-Mese-Arabino-Guanosine Derivatized Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na909

b:49.5
occ:1.00
O A:HOH1060 2.6 35.4 1.0
O A:HOH1061 3.0 33.2 1.0
O A:ASP372 3.0 23.0 1.0
O1 A:GOL907 3.1 43.4 1.0
O A:PHE371 3.2 34.3 1.0
CD A:ARG375 3.6 29.9 1.0
CG A:ARG375 3.7 27.4 1.0
CB A:ARG375 3.7 32.7 1.0
O A:HOH1062 3.8 50.0 1.0
C1 A:GOL907 3.8 42.7 1.0
O A:VAL320 3.8 31.3 1.0
C A:ASP372 3.9 29.0 1.0
N A:ALA376 3.9 30.2 1.0
CB A:ALA376 4.0 22.7 1.0
CB A:ASP372 4.1 26.6 1.0
CA A:ALA376 4.4 30.6 1.0
C A:PHE371 4.4 30.3 1.0
CA A:ASP372 4.5 26.4 1.0
C A:ARG375 4.5 31.2 1.0
O A:HOH1059 4.5 31.7 1.0
O2 A:GOL907 4.6 53.7 1.0
CA A:ARG375 4.6 31.7 1.0
CG A:ASP372 4.7 37.1 1.0
N A:SER373 4.8 26.0 1.0
C A:VAL320 4.9 33.7 1.0
C2 A:GOL907 4.9 49.5 1.0
N A:ASP372 4.9 27.4 1.0
NE A:ARG375 5.0 36.8 1.0

Reference:

S.Jiang, J.Gan, H.Sun, Z.Huang. Crystal Structure of Fragment Dna Polymerase I From Bacillus Stearothermophilus with 2'-Mese-Arabino-Guanosine Derivatized Dna To Be Published.
Page generated: Tue Dec 15 06:56:19 2020

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