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Manganese in PDB 4php: Structure of Human Dna Polymerase Beta Complexed with T in the Template Base Paired with Incoming Non-Hydrolyzable Gtp and Manganese

Enzymatic activity of Structure of Human Dna Polymerase Beta Complexed with T in the Template Base Paired with Incoming Non-Hydrolyzable Gtp and Manganese

All present enzymatic activity of Structure of Human Dna Polymerase Beta Complexed with T in the Template Base Paired with Incoming Non-Hydrolyzable Gtp and Manganese:
2.7.7.7;

Protein crystallography data

The structure of Structure of Human Dna Polymerase Beta Complexed with T in the Template Base Paired with Incoming Non-Hydrolyzable Gtp and Manganese, PDB code: 4php 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) 19.83 / 2.60
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 50.701, 79.327, 55.474, 90.00, 107.58, 90.00
R / Rfree (%) 18.1 / 26.2

Other elements in 4php:

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

Sodium (Na) 2 atoms

Manganese Binding Sites:

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

Manganese binding site 1 out of 2 in 4php

Go back to Manganese Binding Sites List in 4php
Manganese binding site 1 out of 2 in the Structure of Human Dna Polymerase Beta Complexed with T in the Template Base Paired with Incoming Non-Hydrolyzable Gtp and Manganese


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Structure of Human Dna Polymerase Beta Complexed with T in the Template Base Paired with Incoming Non-Hydrolyzable Gtp and Manganese within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn401

b:17.0
occ:1.00
OD2 A:ASP192 1.9 15.8 1.0
OD1 A:ASP190 2.0 15.3 1.0
O A:HOH557 2.1 15.2 1.0
O1A A:XG4405 2.1 12.0 1.0
O1B A:XG4405 2.1 12.3 1.0
O1G A:XG4405 2.4 12.7 1.0
CG A:ASP192 2.9 13.7 1.0
CG A:ASP190 3.1 18.1 1.0
PB A:XG4405 3.2 12.4 1.0
OD1 A:ASP192 3.2 14.8 1.0
PA A:XG4405 3.3 12.8 1.0
PG A:XG4405 3.4 12.4 1.0
OD2 A:ASP190 3.5 21.2 1.0
N3A A:XG4405 3.6 12.3 1.0
O3B A:XG4405 3.8 12.2 1.0
MN A:MN402 3.8 19.1 1.0
O A:HOH558 3.8 16.1 1.0
O2G A:XG4405 3.9 12.3 1.0
O A:ASP190 4.1 18.1 1.0
C5' A:XG4405 4.2 13.0 1.0
C A:ASP190 4.2 18.5 1.0
CB A:ASP192 4.2 11.0 1.0
O5' A:XG4405 4.3 13.0 1.0
CB A:ASP190 4.4 16.2 1.0
N A:ASP190 4.4 15.0 1.0
CA A:GLY179 4.5 13.1 1.0
N A:SER180 4.5 12.4 1.0
OG A:SER180 4.5 9.7 1.0
CA A:ASP190 4.5 13.7 1.0
N A:ASP192 4.6 13.6 1.0
O2A A:XG4405 4.6 12.6 1.0
O2B A:XG4405 4.6 12.2 1.0
N A:MET191 4.7 17.1 1.0
O A:HOH551 4.8 15.3 1.0
C A:MET191 4.8 13.6 1.0
O3G A:XG4405 4.9 12.2 1.0
CA A:MET191 5.0 14.3 1.0

Manganese binding site 2 out of 2 in 4php

Go back to Manganese Binding Sites List in 4php
Manganese binding site 2 out of 2 in the Structure of Human Dna Polymerase Beta Complexed with T in the Template Base Paired with Incoming Non-Hydrolyzable Gtp and Manganese


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Structure of Human Dna Polymerase Beta Complexed with T in the Template Base Paired with Incoming Non-Hydrolyzable Gtp and Manganese within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn402

b:19.1
occ:1.00
OD2 A:ASP256 1.9 21.9 1.0
OD2 A:ASP190 2.2 21.2 1.0
OD1 A:ASP192 2.3 14.8 1.0
O3' P:DC10 2.3 19.4 1.0
O1A A:XG4405 2.5 12.0 1.0
CG A:ASP256 3.0 19.2 1.0
CG A:ASP190 3.2 18.1 1.0
PA A:XG4405 3.4 12.8 1.0
C3' P:DC10 3.4 15.6 1.0
CG A:ASP192 3.4 13.7 1.0
OD1 A:ASP190 3.5 15.3 1.0
O2A A:XG4405 3.7 12.6 1.0
MN A:MN401 3.8 17.0 1.0
O5' A:XG4405 3.8 13.0 1.0
OD2 A:ASP192 3.9 15.8 1.0
OD1 A:ASP256 3.9 18.6 1.0
CB A:ASP256 3.9 13.9 1.0
C5' P:DC10 4.0 16.3 1.0
C4' P:DC10 4.0 18.7 1.0
C5' A:XG4405 4.1 13.0 1.0
O5' P:DC10 4.2 22.1 1.0
OP1 P:DC10 4.3 25.7 1.0
CB A:ASP190 4.5 16.2 1.0
CB A:ASP192 4.7 11.0 1.0
C2' P:DC10 4.7 13.9 1.0
O A:MET191 4.8 17.1 1.0
O A:HOH551 4.9 15.3 1.0
O1G A:XG4405 4.9 12.7 1.0
N3A A:XG4405 4.9 12.3 1.0
P P:DC10 4.9 17.2 1.0

Reference:

M.C.Koag, S.Lee. The Spontaneous Base Substitution Mechanisms of Human Dna Polymerase Beta To Be Published.
Page generated: Sat Oct 5 20:49:33 2024

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