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Sodium in PDB 4o9m: Human Dna Polymerase Beta Complexed with Adenylated Tetrahydrofuran (Abasic Site) Containing Dna

Enzymatic activity of Human Dna Polymerase Beta Complexed with Adenylated Tetrahydrofuran (Abasic Site) Containing Dna

All present enzymatic activity of Human Dna Polymerase Beta Complexed with Adenylated Tetrahydrofuran (Abasic Site) Containing Dna:
2.7.7.7;

Protein crystallography data

The structure of Human Dna Polymerase Beta Complexed with Adenylated Tetrahydrofuran (Abasic Site) Containing Dna, PDB code: 4o9m was solved by M.Caglayan, V.K.Batra, A.Sassa, R.Prasad, S.H.Wilson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 23.51 / 2.29
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 54.627, 78.873, 54.324, 90.00, 105.94, 90.00
R / Rfree (%) 19.3 / 26.1

Sodium Binding Sites:

The binding sites of Sodium atom in the Human Dna Polymerase Beta Complexed with Adenylated Tetrahydrofuran (Abasic Site) Containing Dna (pdb code 4o9m). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Human Dna Polymerase Beta Complexed with Adenylated Tetrahydrofuran (Abasic Site) Containing Dna, PDB code: 4o9m:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 4o9m

Go back to Sodium Binding Sites List in 4o9m
Sodium binding site 1 out of 2 in the Human Dna Polymerase Beta Complexed with Adenylated Tetrahydrofuran (Abasic Site) Containing Dna


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Human Dna Polymerase Beta Complexed with Adenylated Tetrahydrofuran (Abasic Site) Containing Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na401

b:13.3
occ:1.00
OP1 C:DG9 2.2 13.9 1.0
O A:THR101 2.3 13.8 1.0
O A:VAL103 2.4 10.7 1.0
O C:HOH101 2.5 6.6 1.0
O A:ILE106 2.6 9.0 1.0
O C:HOH104 2.8 16.9 1.0
C A:VAL103 3.2 10.9 1.0
C A:THR101 3.4 12.9 1.0
P C:DG9 3.4 13.3 1.0
C A:ILE106 3.5 11.1 1.0
O A:HOH639 3.6 14.6 1.0
OP2 C:DG9 3.7 19.4 1.0
N A:ILE106 3.8 10.5 1.0
CA A:SER104 3.8 9.5 1.0
N A:SER104 3.8 12.2 1.0
N A:GLY105 3.9 9.9 1.0
O A:HOH501 3.9 28.3 1.0
CA A:THR101 4.0 11.4 1.0
CA A:ILE106 4.1 12.6 1.0
N A:VAL103 4.2 9.1 1.0
C A:ARG102 4.2 14.0 1.0
C A:SER104 4.2 12.2 1.0
CA A:VAL103 4.3 11.9 1.0
N A:ARG102 4.4 18.1 1.0
O5' C:DG9 4.4 14.4 1.0
N A:GLY107 4.4 12.0 1.0
O A:ARG102 4.4 12.2 1.0
O3' C:DC8 4.5 13.5 1.0
CB A:THR101 4.5 14.2 1.0
CA A:ARG102 4.6 16.8 1.0
C A:GLY105 4.6 13.9 1.0
CB A:ILE106 4.7 11.6 1.0
CA A:GLY107 4.7 12.1 1.0
CA A:GLY105 4.8 13.8 1.0
O A:LEU100 4.9 11.6 1.0

Sodium binding site 2 out of 2 in 4o9m

Go back to Sodium Binding Sites List in 4o9m
Sodium binding site 2 out of 2 in the Human Dna Polymerase Beta Complexed with Adenylated Tetrahydrofuran (Abasic Site) Containing Dna


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Human Dna Polymerase Beta Complexed with Adenylated Tetrahydrofuran (Abasic Site) Containing Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na402

b:25.1
occ:1.00
O A:VAL65 2.1 20.9 1.0
O A:LYS60 2.5 24.7 1.0
O A:LEU62 2.6 25.6 1.0
O D:HOH111 2.6 24.0 1.0
O A:HOH632 2.6 28.9 1.0
OP1 D:DC3 2.8 26.5 1.0
C A:VAL65 3.1 20.9 1.0
C A:LYS60 3.5 22.9 1.0
N A:VAL65 3.5 22.0 1.0
P D:DC3 3.6 17.1 1.0
OP2 D:DC3 3.6 18.1 1.0
C A:LEU62 3.7 18.2 1.0
CA A:VAL65 3.8 20.0 1.0
CA A:LYS60 4.1 22.1 1.0
N A:GLY64 4.1 28.2 1.0
CB A:VAL65 4.2 21.1 1.0
N A:GLY66 4.2 18.9 1.0
N A:LEU62 4.2 22.1 1.0
O3' D:DT2 4.3 19.7 1.0
CA A:PRO63 4.3 18.7 1.0
CG A:LYS60 4.4 26.4 1.0
C A:LYS61 4.5 23.6 1.0
N A:PRO63 4.5 23.8 1.0
CA A:GLY66 4.5 17.5 1.0
C A:PRO63 4.5 26.3 1.0
C A:GLY64 4.5 23.6 1.0
N A:LYS61 4.5 23.1 1.0
CA A:LEU62 4.6 24.4 1.0
CB A:LYS60 4.8 23.2 1.0
O A:ALA59 4.8 18.0 1.0
CA A:LYS61 4.8 26.8 1.0
O A:LYS61 4.9 26.0 1.0
CA A:GLY64 4.9 22.0 1.0

Reference:

M.Caglayan, V.K.Batra, A.Sassa, R.Prasad, S.H.Wilson. Role of Polymerase Beta in Complementing Aprataxin Deficiency During Abasic-Site Base Excision Repair. Nat.Struct.Mol.Biol. V. 21 497 2014.
ISSN: ISSN 1545-9993
PubMed: 24777061
DOI: 10.1038/NSMB.2818
Page generated: Tue Dec 15 06:56:38 2020

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