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Manganese in PDB 4ymo: Structure of Human Dna Polymerase Beta Complexed with N7BG in the Template Opposite to Incoming Non-Hydrolyzable Ctp 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 Ctp 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 Ctp 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 Ctp with Manganese in the Active Site, PDB code: 4ymo 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) 19.93 / 2.15
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 50.728, 79.170, 55.634, 90.00, 107.23, 90.00
R / Rfree (%) 19.4 / 22.6

Other elements in 4ymo:

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

Fluorine (F) 1 atom
Sodium (Na) 2 atoms

Manganese Binding Sites:

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

Manganese binding site 1 out of 2 in 4ymo

Go back to Manganese Binding Sites List in 4ymo
Manganese 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 Ctp with Manganese in the Active Site


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 N7BG in the Template Opposite to Incoming Non-Hydrolyzable Ctp with Manganese in the Active Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn401

b:12.5
occ:1.00
 OD1 A:ASP190 2.0 15.0 1.0
OD2 A:ASP192 2.0 11.6 1.0
O1B A:0KX405 2.1 12.8 1.0
O1G A:0KX405 2.2 13.3 1.0
O2A A:0KX405 2.2 15.1 1.0
O A:HOH559 2.4 11.3 1.0
CG A:ASP192 3.1 13.1 1.0
PB A:0KX405 3.1 14.1 1.0
CG A:ASP190 3.1 17.0 1.0
PA A:0KX405 3.3 13.9 1.0
OD1 A:ASP192 3.4 19.2 1.0
PG A:0KX405 3.4 15.1 1.0
N3A A:0KX405 3.6 14.2 1.0
MN A:MN402 3.6 18.1 1.0
OD2 A:ASP190 3.6 15.5 1.0
O3B A:0KX405 3.7 12.8 1.0
O A:HOH599 4.0 18.4 1.0
O A:ASP190 4.1 15.4 1.0
C5' A:0KX405 4.1 12.6 1.0
O2G A:0KX405 4.2 11.8 1.0
O A:HOH547 4.2 13.8 1.0
C A:ASP190 4.2 15.2 1.0
N A:ASP190 4.3 11.5 1.0
O5' A:0KX405 4.3 13.1 1.0
OG A:SER180 4.4 15.4 1.0
CB A:ASP190 4.4 13.9 1.0
CB A:ASP192 4.4 17.3 1.0
N A:SER180 4.4 14.0 1.0
CA A:GLY179 4.5 13.8 1.0
CA A:ASP190 4.5 13.6 1.0
O3G A:0KX405 4.6 16.6 1.0
O2B A:0KX405 4.6 12.8 1.0
O1A A:0KX405 4.6 14.7 1.0
N A:ASP192 4.7 17.8 1.0
N A:MET191 4.8 12.4 1.0
O P:HOH106 4.8 14.4 1.0
C A:MET191 4.9 15.0 1.0

Manganese binding site 2 out of 2 in 4ymo

Go back to Manganese Binding Sites List in 4ymo
Manganese 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 Ctp with Manganese in the Active Site


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 N7BG in the Template Opposite to Incoming Non-Hydrolyzable Ctp with Manganese in the Active Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn402

b:18.1
occ:1.00
 OD1 A:ASP192 2.1 19.2 1.0
OD2 A:ASP190 2.1 15.5 1.0
O2A A:0KX405 2.3 15.1 1.0
O P:HOH106 2.3 14.4 1.0
O3' P:DA10 2.3 14.3 1.0
OD1 A:ASP256 2.4 17.5 1.0
CG A:ASP190 3.1 17.0 1.0
CG A:ASP192 3.2 13.1 1.0
CG A:ASP256 3.2 22.8 1.0
OD2 A:ASP256 3.3 26.5 1.0
OD1 A:ASP190 3.3 15.0 1.0
PA A:0KX405 3.4 13.9 1.0
C3' P:DA10 3.5 15.4 1.0
OD2 A:ASP192 3.6 11.6 1.0
MN A:MN401 3.6 12.5 1.0
O5' A:0KX405 3.7 13.1 1.0
O1A A:0KX405 3.9 14.7 1.0
C5' A:0KX405 4.0 12.6 1.0
C4' P:DA10 4.2 17.8 1.0
C5' P:DA10 4.3 15.3 1.0
OP1 P:DA10 4.4 21.4 1.0
O A:HOH599 4.4 18.4 1.0
CB A:ASP192 4.4 17.3 1.0
CB A:ASP190 4.5 13.9 1.0
O5' P:DA10 4.6 16.1 1.0
CB A:ASP256 4.6 22.5 1.0
C2' P:DA10 4.7 17.3 1.0
O A:MET191 4.8 15.4 1.0
O1G A:0KX405 4.9 13.3 1.0
NH2 A:ARG254 4.9 27.6 1.0
N3A A:0KX405 5.0 14.2 1.0
CA A:ASP192 5.0 17.1 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: Sat Oct 5 23:02:03 2024

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