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Sodium in PDB 4z6e: Structure of Human Dna Polymerase Beta 279NA Mutant Complexed with G in the Template Base Paired with Incoming Non-Hydrolyzable Ttp and Manganese

Enzymatic activity of Structure of Human Dna Polymerase Beta 279NA Mutant Complexed with G in the Template Base Paired with Incoming Non-Hydrolyzable Ttp and Manganese

All present enzymatic activity of Structure of Human Dna Polymerase Beta 279NA Mutant Complexed with G in the Template Base Paired with Incoming Non-Hydrolyzable Ttp and Manganese:
2.7.7.7;

Protein crystallography data

The structure of Structure of Human Dna Polymerase Beta 279NA Mutant Complexed with G in the Template Base Paired with Incoming Non-Hydrolyzable Ttp and Manganese, PDB code: 4z6e was solved by M.-C.Koag, S.Lee, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.94 / 2.75
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 50.562, 79.567, 55.143, 90.00, 107.64, 90.00
R / Rfree (%) 17.8 / 24.8

Other elements in 4z6e:

The structure of Structure of Human Dna Polymerase Beta 279NA Mutant Complexed with G in the Template Base Paired with Incoming Non-Hydrolyzable Ttp and Manganese also contains other interesting chemical elements:

Manganese (Mn) 2 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Structure of Human Dna Polymerase Beta 279NA Mutant Complexed with G in the Template Base Paired with Incoming Non-Hydrolyzable Ttp and Manganese (pdb code 4z6e). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Structure of Human Dna Polymerase Beta 279NA Mutant Complexed with G in the Template Base Paired with Incoming Non-Hydrolyzable Ttp and Manganese, PDB code: 4z6e:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 4z6e

Go back to Sodium Binding Sites List in 4z6e
Sodium binding site 1 out of 2 in the Structure of Human Dna Polymerase Beta 279NA Mutant Complexed with G in the Template Base Paired with Incoming Non-Hydrolyzable Ttp and Manganese


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure of Human Dna Polymerase Beta 279NA Mutant Complexed with G in the Template Base Paired with Incoming Non-Hydrolyzable Ttp and Manganese within 5.0Å range:
probe atom residue distance (Å) B Occ
P:Na402

b:25.2
occ:1.00
 O A:THR101 2.3 20.0 1.0
OP1 P:DG9 2.4 21.7 1.0
O A:ILE106 2.6 19.2 1.0
O A:VAL103 3.0 23.2 1.0
OP2 P:DG9 3.2 18.7 1.0
P P:DG9 3.2 21.8 1.0
C A:THR101 3.5 18.5 1.0
C A:ILE106 3.7 21.8 1.0
C A:VAL103 3.9 19.0 1.0
CA A:SER104 4.1 19.4 1.0
N A:ILE106 4.2 19.1 1.0
O3' P:DC8 4.2 23.4 1.0
N A:GLY105 4.3 20.9 1.0
C A:ARG102 4.3 19.3 1.0
CA A:THR101 4.3 20.5 1.0
N A:SER104 4.3 17.8 1.0
O A:ARG102 4.4 23.1 1.0
O5' P:DG9 4.4 18.8 1.0
CA A:ILE106 4.4 21.3 1.0
N A:ARG102 4.4 14.8 1.0
CA A:ARG102 4.6 17.3 1.0
C A:SER104 4.6 22.3 1.0
N A:VAL103 4.6 19.1 1.0
N A:GLY107 4.7 19.1 1.0
CB A:THR101 4.8 18.0 1.0
CB A:ILE106 4.8 19.0 1.0
CA A:VAL103 4.9 19.8 1.0
CA A:GLY107 4.9 21.1 1.0

Sodium binding site 2 out of 2 in 4z6e

Go back to Sodium Binding Sites List in 4z6e
Sodium binding site 2 out of 2 in the Structure of Human Dna Polymerase Beta 279NA Mutant Complexed with G in the Template Base Paired with Incoming Non-Hydrolyzable Ttp and Manganese


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Structure of Human Dna Polymerase Beta 279NA Mutant Complexed with G in the Template Base Paired with Incoming Non-Hydrolyzable Ttp and Manganese within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na101

b:35.6
occ:1.00
 OP1 D:DC3 2.4 40.5 1.0
O A:LYS60 2.4 31.4 1.0
O A:LEU62 2.6 34.7 1.0
O A:HOH539 2.6 37.6 1.0
O A:VAL65 2.6 31.0 1.0
C A:LYS60 3.5 30.8 1.0
C A:LEU62 3.5 34.6 1.0
C A:VAL65 3.7 30.2 1.0
P D:DC3 3.7 39.2 1.0
OP2 D:DC3 4.1 38.9 1.0
N A:LEU62 4.2 30.5 1.0
N A:VAL65 4.2 25.7 1.0
CA A:PRO63 4.2 31.8 1.0
N A:PRO63 4.3 35.9 1.0
CA A:LYS60 4.3 32.0 1.0
C A:LYS61 4.3 29.6 1.0
CA A:VAL65 4.4 30.6 1.0
CG A:LYS60 4.5 29.2 1.0
CA A:LEU62 4.5 27.8 1.0
N A:LYS61 4.5 28.1 1.0
O5' D:DC3 4.5 46.1 1.0
N A:GLY64 4.6 32.0 1.0
N A:GLY66 4.6 34.2 1.0
CB A:VAL65 4.7 32.6 1.0
CA A:LYS61 4.7 30.4 1.0
C A:PRO63 4.7 35.8 1.0
O A:LYS61 4.8 28.2 1.0
CA A:GLY66 4.8 34.0 1.0
O3' D:DT2 4.8 28.8 1.0
O A:ALA59 5.0 33.6 1.0
CB A:LYS60 5.0 29.0 1.0

Reference:

M.C.Koag, S.Lee. Insights Into the Effect of Minor Groove Interactions and Metal Cofactors on Mutagenic Replication By Human Dna Polymerase Beta. Biochem. J. V. 475 571 2018.
ISSN: ESSN 1470-8728
PubMed: 29301983
DOI: 10.1042/BCJ20170787
Page generated: Mon Oct 7 19:37:48 2024

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