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Sodium in PDB 3lwm: Structure of the Large Fragment of Thermus Aquaticus Dna Polymerase I in Complex with A Blunt-Ended Dna and Ddatp

Enzymatic activity of Structure of the Large Fragment of Thermus Aquaticus Dna Polymerase I in Complex with A Blunt-Ended Dna and Ddatp

All present enzymatic activity of Structure of the Large Fragment of Thermus Aquaticus Dna Polymerase I in Complex with A Blunt-Ended Dna and Ddatp:
2.7.7.7;

Protein crystallography data

The structure of Structure of the Large Fragment of Thermus Aquaticus Dna Polymerase I in Complex with A Blunt-Ended Dna and Ddatp, PDB code: 3lwm was solved by A.Marx, K.Diederichs, S.Obeid, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.45 / 2.19
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 109.592, 109.592, 91.037, 90.00, 90.00, 120.00
R / Rfree (%) 18.3 / 22.8

Other elements in 3lwm:

The structure of Structure of the Large Fragment of Thermus Aquaticus Dna Polymerase I in Complex with A Blunt-Ended Dna and Ddatp also contains other interesting chemical elements:

Magnesium (Mg) 1 atom

Sodium Binding Sites:

The binding sites of Sodium atom in the Structure of the Large Fragment of Thermus Aquaticus Dna Polymerase I in Complex with A Blunt-Ended Dna and Ddatp (pdb code 3lwm). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Structure of the Large Fragment of Thermus Aquaticus Dna Polymerase I in Complex with A Blunt-Ended Dna and Ddatp, PDB code: 3lwm:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in 3lwm

Go back to Sodium Binding Sites List in 3lwm
Sodium binding site 1 out of 4 in the Structure of the Large Fragment of Thermus Aquaticus Dna Polymerase I in Complex with A Blunt-Ended Dna and Ddatp


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure of the Large Fragment of Thermus Aquaticus Dna Polymerase I in Complex with A Blunt-Ended Dna and Ddatp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na836

b:39.5
occ:1.00
 OD1 A:ASN750 3.1 31.7 1.0
O A:HOH162 3.2 50.9 1.0
OE1 A:GLN754 3.2 32.3 1.0
OE2 A:GLU615 3.3 66.3 1.0
CE1 A:TYR671 3.5 44.3 1.0
OE1 A:GLU615 3.5 60.6 1.0
CB A:GLN754 3.6 21.8 1.0
CD A:GLU615 3.7 59.7 1.0
O2 C:DT205 3.7 37.3 1.0
ND2 A:ASN750 3.9 20.7 1.0
CG A:ASN750 3.9 28.0 1.0
CD A:GLN754 4.0 22.5 1.0
CG A:GLN754 4.0 22.5 1.0
CD1 A:TYR671 4.2 44.2 1.0
CD2 A:LEU670 4.2 54.1 1.0
CA A:GLN754 4.3 24.4 1.0
C2 C:DT205 4.4 37.4 1.0
NH2 A:ARG573 4.5 26.0 1.0
C1' C:DT205 4.5 28.3 1.0
CZ A:TYR671 4.5 43.3 1.0
OH A:TYR671 4.6 38.1 1.0
CG A:LEU670 4.7 52.2 1.0
N A:GLN754 4.7 22.2 1.0
N1 C:DT205 4.8 37.6 1.0
CG A:GLU615 4.9 48.1 1.0

Sodium binding site 2 out of 4 in 3lwm

Go back to Sodium Binding Sites List in 3lwm
Sodium binding site 2 out of 4 in the Structure of the Large Fragment of Thermus Aquaticus Dna Polymerase I in Complex with A Blunt-Ended Dna and Ddatp


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Structure of the Large Fragment of Thermus Aquaticus Dna Polymerase I in Complex with A Blunt-Ended Dna and Ddatp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na837

b:54.2
occ:1.00
 OE2 A:GLU745 2.9 38.8 1.0
O A:HOH84 3.2 34.0 1.0
NE A:ARG741 3.3 30.1 1.0
O A:HOH86 3.6 49.1 1.0
CD A:GLU745 3.7 36.6 1.0
OE1 A:GLU745 3.8 34.2 1.0
O A:HOH26 3.9 38.4 1.0
CD A:ARG741 3.9 32.4 1.0
CZ A:ARG741 4.2 36.4 1.0
NH2 A:ARG741 4.3 33.1 1.0
O A:HOH14 4.4 45.4 1.0
CG A:ARG741 4.5 34.2 1.0
NH1 A:ARG715 4.8 43.5 1.0

Sodium binding site 3 out of 4 in 3lwm

Go back to Sodium Binding Sites List in 3lwm
Sodium binding site 3 out of 4 in the Structure of the Large Fragment of Thermus Aquaticus Dna Polymerase I in Complex with A Blunt-Ended Dna and Ddatp


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Structure of the Large Fragment of Thermus Aquaticus Dna Polymerase I in Complex with A Blunt-Ended Dna and Ddatp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na5

b:88.2
occ:1.00
 OE1 A:GLU774 3.5 69.3 1.0
CD A:GLU774 4.7 71.0 1.0

Sodium binding site 4 out of 4 in 3lwm

Go back to Sodium Binding Sites List in 3lwm
Sodium binding site 4 out of 4 in the Structure of the Large Fragment of Thermus Aquaticus Dna Polymerase I in Complex with A Blunt-Ended Dna and Ddatp


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Structure of the Large Fragment of Thermus Aquaticus Dna Polymerase I in Complex with A Blunt-Ended Dna and Ddatp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na6

b:76.7
occ:1.00
 O A:HOH112 3.0 42.2 1.0
O A:HOH31 3.2 31.1 1.0
OD1 A:ASP355 3.3 41.3 1.0
CG A:ASP355 3.6 42.9 1.0
NZ A:LYS354 3.6 32.7 1.0
N A:ASP355 3.6 30.4 1.0
O A:HOH842 3.7 25.7 1.0
CA A:LEU352 3.7 26.7 1.0
CB A:LYS354 3.8 31.5 1.0
O A:HOH77 3.8 27.5 1.0
C A:LEU352 3.9 26.6 1.0
O A:LEU352 3.9 22.2 1.0
CD2 A:LEU352 3.9 30.0 1.0
OD2 A:ASP355 4.0 48.5 1.0
CE A:LYS354 4.0 31.3 1.0
CB A:LEU352 4.1 26.7 1.0
N A:LYS354 4.1 32.6 1.0
CB A:ASP355 4.2 35.9 1.0
CA A:LYS354 4.3 32.7 1.0
O A:HOH38 4.3 30.9 1.0
CG A:LYS354 4.3 29.9 1.0
O A:HOH10 4.3 33.3 1.0
C A:LYS354 4.4 30.9 1.0
CA A:ASP355 4.4 31.9 1.0
N A:ALA353 4.6 26.6 1.0
CG A:LEU352 4.7 33.8 1.0
O A:HOH75 4.7 30.4 1.0
CD A:LYS354 4.8 32.8 1.0
OD2 A:ASP372 4.9 36.8 1.0
C A:ALA353 4.9 35.6 1.0
N A:LEU352 5.0 29.6 1.0

Reference:

S.Obeid, N.Blatter, R.Kranaster, A.Schnur, K.Diederichs, W.Welte, A.Marx. Replication Through An Abasic Dna Lesion: Structural Basis For Adenine Selectivity Embo J. V. 29 1738 2010.
ISSN: ISSN 0261-4189
PubMed: 20400942
DOI: 10.1038/EMBOJ.2010.64
Page generated: Mon Oct 7 11:24:36 2024

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