Atomistry » Sodium » PDB 4yil-4z48 » 4yn4
Atomistry »
  Sodium »
    PDB 4yil-4z48 »
      4yn4 »

Sodium in PDB 4yn4: Structure of Human Dna Polymerase Beta Complexed with N7BG in the Template Opposite to Incoming Non-Hydrolyzable Dttp with Manganese in the Active Site

Enzymatic activity of Structure of Human Dna Polymerase Beta Complexed with N7BG in the Template Opposite to Incoming Non-Hydrolyzable Dttp with Manganese in the Active Site

All present enzymatic activity of Structure of Human Dna Polymerase Beta Complexed with N7BG in the Template Opposite to Incoming Non-Hydrolyzable Dttp with Manganese in the Active Site:
2.7.7.7;

Protein crystallography data

The structure of Structure of Human Dna Polymerase Beta Complexed with N7BG in the Template Opposite to Incoming Non-Hydrolyzable Dttp with Manganese in the Active Site, PDB code: 4yn4 was solved by S.Lee, M.-C.Koag, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.80 / 2.24
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 54.774, 79.179, 55.031, 90.00, 106.53, 90.00
R / Rfree (%) 20.3 / 25.5

Other elements in 4yn4:

The structure of Structure of Human Dna Polymerase Beta Complexed with N7BG in the Template Opposite to Incoming Non-Hydrolyzable Dttp with Manganese in the Active Site also contains other interesting chemical elements:

Fluorine (F) 1 atom
Manganese (Mn) 2 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Structure of Human Dna Polymerase Beta Complexed with N7BG in the Template Opposite to Incoming Non-Hydrolyzable Dttp with Manganese in the Active Site (pdb code 4yn4). 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 Complexed with N7BG in the Template Opposite to Incoming Non-Hydrolyzable Dttp with Manganese in the Active Site, PDB code: 4yn4:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 4yn4

Go back to Sodium Binding Sites List in 4yn4
Sodium binding site 1 out of 2 in the Structure of Human Dna Polymerase Beta Complexed with N7BG in the Template Opposite to Incoming Non-Hydrolyzable Dttp with Manganese in the Active Site


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 Complexed with N7BG in the Template Opposite to Incoming Non-Hydrolyzable Dttp with Manganese in the Active Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na402

b:33.2
occ:1.00
 O D:HOH104 2.4 31.8 1.0
O A:VAL65 2.4 34.5 1.0
O A:HOH546 2.4 36.3 1.0
O A:LEU62 2.5 34.4 1.0
O A:LYS60 2.5 35.7 1.0
OP1 D:DC3 2.6 33.3 1.0
C A:LEU62 3.4 33.5 1.0
C A:VAL65 3.5 29.9 1.0
C A:LYS60 3.5 36.4 1.0
N A:VAL65 3.7 30.5 1.0
P D:DC3 3.7 25.9 1.0
N A:LEU62 4.0 34.0 1.0
CA A:VAL65 4.0 26.0 1.0
OP2 D:DC3 4.0 25.8 1.0
C A:LYS61 4.0 36.5 1.0
N A:GLY64 4.1 32.0 1.0
N A:PRO63 4.1 32.1 1.0
CA A:PRO63 4.2 34.2 1.0
CB A:VAL65 4.3 29.1 1.0
CA A:LYS60 4.3 33.0 1.0
O A:LYS61 4.3 40.7 1.0
CA A:LEU62 4.3 35.9 1.0
N A:LYS61 4.4 31.8 1.0
CA A:LYS61 4.5 33.8 1.0
N A:GLY66 4.5 22.8 1.0
C A:PRO63 4.5 30.4 1.0
CG A:LYS60 4.5 34.8 1.0
O3' D:DT2 4.6 30.5 1.0
C A:GLY64 4.8 27.5 1.0
CA A:GLY66 4.8 23.7 1.0
O5' D:DC3 4.9 25.2 1.0
O A:ALA59 5.0 32.0 1.0

Sodium binding site 2 out of 2 in 4yn4

Go back to Sodium Binding Sites List in 4yn4
Sodium binding site 2 out of 2 in the Structure of Human Dna Polymerase Beta Complexed with N7BG in the Template Opposite to Incoming Non-Hydrolyzable Dttp with Manganese in the Active Site


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 Complexed with N7BG in the Template Opposite to Incoming Non-Hydrolyzable Dttp with Manganese in the Active Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na403

b:19.4
occ:1.00
 O A:THR101 2.3 24.6 1.0
OP1 P:DG9 2.4 20.8 1.0
O A:ILE106 2.4 19.2 1.0
O A:VAL103 2.5 20.4 1.0
O A:HOH582 2.5 23.9 1.0
O P:HOH111 2.6 22.3 1.0
C A:THR101 3.2 22.7 1.0
C A:VAL103 3.3 23.4 1.0
O A:HOH583 3.3 17.4 1.0
C A:ILE106 3.4 20.1 1.0
P P:DG9 3.6 22.8 1.0
N A:ILE106 3.8 19.2 1.0
CA A:SER104 3.8 20.5 1.0
CA A:THR101 3.9 20.4 1.0
N A:SER104 3.9 20.3 1.0
OP2 P:DG9 3.9 22.7 1.0
N A:GLY105 3.9 14.5 1.0
N A:VAL103 4.1 21.6 1.0
CA A:ILE106 4.1 18.5 1.0
C A:ARG102 4.2 23.9 1.0
N A:ARG102 4.2 23.9 1.0
C A:SER104 4.3 17.1 1.0
CA A:VAL103 4.3 18.8 1.0
N A:GLY107 4.4 22.1 1.0
CB A:THR101 4.4 22.4 1.0
CB A:ILE106 4.5 17.1 1.0
CA A:ARG102 4.5 23.0 1.0
O3' P:DC8 4.6 23.0 1.0
O5' P:DG9 4.6 24.1 1.0
O A:ARG102 4.6 23.8 1.0
CA A:GLY107 4.6 19.5 1.0
C A:GLY105 4.6 17.5 1.0
O P:HOH109 4.8 26.2 1.0
O A:LEU100 4.9 18.7 1.0
CA A:GLY105 4.9 18.9 1.0

Reference:

Y.Kou, M.C.Koag, S.Lee. Structural and Kinetic Studies of the Effect of Guanine-N7 Alkylation and Metal Cofactors on Dna Replication. Biochemistry 2018.
ISSN: ISSN 1520-4995
PubMed: 29957995
DOI: 10.1021/ACS.BIOCHEM.8B00331
Page generated: Mon Oct 7 19:33:16 2024

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy