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Sodium in PDB 4z6d: Structure of Human Dna Polymerase Beta 279NA Mutant Complexed with G in the Template Base Paired with Incoming Non-Hydrolyzable Ttp

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

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:
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, PDB code: 4z6d 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) 19.85 / 2.51
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 54.283, 79.382, 54.859, 90.00, 110.18, 90.00
R / Rfree (%) 19.8 / 27

Other elements in 4z6d:

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

Magnesium (Mg) 1 atom

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 (pdb code 4z6d). 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, PDB code: 4z6d:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 4z6d

Go back to Sodium Binding Sites List in 4z6d
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


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na401

b:38.0
occ:1.00
 O A:LYS60 2.5 27.4 1.0
OP1 D:DC3 2.9 33.3 1.0
O A:LEU62 3.1 25.3 1.0
O A:VAL65 3.1 28.7 1.0
C A:LYS60 3.7 28.0 1.0
C A:LEU62 3.9 25.2 1.0
P D:DC3 4.0 26.2 1.0
O A:LYS61 4.0 25.2 1.0
C A:LYS61 4.0 27.0 1.0
OP2 D:DC3 4.1 24.4 1.0
C A:VAL65 4.3 27.3 1.0
N A:LEU62 4.4 22.5 1.0
CA A:PRO63 4.4 22.9 1.0
N A:PRO63 4.4 23.0 1.0
CA A:LYS61 4.5 30.4 1.0
N A:GLY64 4.5 28.8 1.0
N A:LYS61 4.5 27.6 1.0
N A:VAL65 4.6 27.0 1.0
CG A:LYS60 4.7 25.3 1.0
CA A:LYS60 4.7 26.8 1.0
CA A:LEU62 4.8 23.8 1.0
O5' D:DC3 4.9 27.4 1.0
CA A:VAL65 4.9 26.9 1.0

Sodium binding site 2 out of 2 in 4z6d

Go back to Sodium Binding Sites List in 4z6d
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


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na402

b:21.5
occ:1.00
 OP1 P:DG9 2.3 17.7 1.0
O A:THR101 2.3 24.0 1.0
O A:VAL103 2.5 16.2 1.0
O P:HOH111 2.6 13.9 1.0
O A:ILE106 2.7 19.0 1.0
C A:THR101 3.4 19.4 1.0
C A:VAL103 3.4 13.6 1.0
P P:DG9 3.5 15.1 1.0
C A:ILE106 3.7 18.1 1.0
OP2 P:DG9 3.8 21.8 1.0
CA A:SER104 3.8 9.9 1.0
O A:HOH550 3.9 27.2 1.0
N A:SER104 3.9 15.8 1.0
N A:GLY105 3.9 17.2 1.0
N A:ILE106 4.0 12.9 1.0
CA A:THR101 4.1 23.6 1.0
N A:VAL103 4.1 13.5 1.0
C A:ARG102 4.2 17.3 1.0
N A:ARG102 4.3 20.7 1.0
C A:SER104 4.3 14.6 1.0
CA A:ILE106 4.3 13.7 1.0
O5' P:DG9 4.4 19.7 1.0
CA A:VAL103 4.4 13.8 1.0
CA A:ARG102 4.5 17.8 1.0
O A:ARG102 4.6 14.9 1.0
CB A:THR101 4.6 22.3 1.0
N A:GLY107 4.6 14.3 1.0
O3' P:DC8 4.7 18.7 1.0
CB A:ILE106 4.8 16.9 1.0
C A:GLY105 4.8 13.5 1.0
CA A:GLY107 4.9 15.2 1.0
O A:HOH541 4.9 30.1 1.0
CA A:GLY105 5.0 16.9 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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