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Magnesium in PDB 5vzf: Post-Catalytic Complex of Human Polymerase Mu (W434A) Mutant with Incoming Dttp

Enzymatic activity of Post-Catalytic Complex of Human Polymerase Mu (W434A) Mutant with Incoming Dttp

All present enzymatic activity of Post-Catalytic Complex of Human Polymerase Mu (W434A) Mutant with Incoming Dttp:
2.7.7.7;

Protein crystallography data

The structure of Post-Catalytic Complex of Human Polymerase Mu (W434A) Mutant with Incoming Dttp, PDB code: 5vzf was solved by A.F.Moon, J.M.Pryor, D.A.Ramsden, T.A.Kunkel, K.Bebenek, L.C.Pedersen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 32.79 / 1.65
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 59.866, 68.690, 110.224, 90.00, 90.00, 90.00
R / Rfree (%) 16.9 / 19.5

Other elements in 5vzf:

The structure of Post-Catalytic Complex of Human Polymerase Mu (W434A) Mutant with Incoming Dttp also contains other interesting chemical elements:

Sodium (Na) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Post-Catalytic Complex of Human Polymerase Mu (W434A) Mutant with Incoming Dttp (pdb code 5vzf). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Post-Catalytic Complex of Human Polymerase Mu (W434A) Mutant with Incoming Dttp, PDB code: 5vzf:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 5vzf

Go back to Magnesium Binding Sites List in 5vzf
Magnesium binding site 1 out of 4 in the Post-Catalytic Complex of Human Polymerase Mu (W434A) Mutant with Incoming Dttp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Post-Catalytic Complex of Human Polymerase Mu (W434A) Mutant with Incoming Dttp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg702

b:7.1
occ:1.00
 O2A P:TTP701 1.9 3.6 0.4
O2G A:TTP701 2.0 2.7 0.6
OD2 A:ASP332 2.0 6.6 1.0
OD1 A:ASP330 2.1 8.6 1.0
O A:HOH898 2.1 9.5 1.0
O3G P:TTP701 2.1 6.3 0.4
O2B P:TTP701 2.1 4.2 0.4
OP1 P:DT5 2.1 6.4 0.6
O2B A:TTP701 2.2 9.3 0.6
PB P:TTP701 3.0 6.6 0.4
PA P:TTP701 3.1 7.2 0.4
CG A:ASP332 3.1 7.8 1.0
CG A:ASP330 3.1 17.8 1.0
PG P:TTP701 3.3 10.3 0.4
O3A P:TTP701 3.3 5.3 0.4
PG A:TTP701 3.3 7.5 0.6
PB A:TTP701 3.4 12.9 0.6
O3B P:TTP701 3.4 8.0 0.4
OD1 A:ASP332 3.5 9.2 1.0
MG A:MG703 3.5 2.3 0.4
NA A:NA705 3.5 22.0 0.6
OD2 A:ASP330 3.5 23.0 1.0
P P:DT5 3.5 6.0 0.6
O3B A:TTP701 3.5 6.8 0.6
O2G P:TTP701 4.0 16.0 0.4
C5' P:TTP701 4.1 3.3 0.4
O P:HOH801 4.1 23.2 1.0
O A:ASP330 4.1 7.2 1.0
O5' P:TTP701 4.1 1.7 0.4
O5' P:DT5 4.2 9.8 0.6
O A:HOH815 4.2 8.0 1.0
O1A P:TTP701 4.2 8.2 0.4
C5' P:DT5 4.2 10.0 0.6
O3G A:TTP701 4.2 8.7 0.6
N A:GLY320 4.3 5.2 1.0
ND1 A:HIS329 4.4 16.8 0.4
C A:ASP330 4.4 7.3 1.0
O1B A:TTP701 4.4 13.6 0.6
O1G A:TTP701 4.4 7.8 0.6
O1B P:TTP701 4.4 4.6 0.4
O3' P:DA4 4.4 6.9 0.6
CB A:ASP332 4.4 6.2 1.0
OP2 P:DT5 4.5 6.3 0.6
O1G P:TTP701 4.5 16.9 0.4
CB A:ASP330 4.5 8.9 1.0
O3A A:TTP701 4.5 16.9 0.6
CE1 A:HIS329 4.5 18.6 0.4
CA A:GLY319 4.6 5.5 1.0
CA A:ASP330 4.8 9.6 1.0
O P:HOH818 4.8 9.7 0.4
N A:ASP330 4.8 10.0 1.0
O A:HOH864 4.8 13.4 0.4
N A:ASP332 4.9 6.2 1.0
N A:VAL331 5.0 7.3 1.0
O P:HOH819 5.0 20.1 0.6

Magnesium binding site 2 out of 4 in 5vzf

Go back to Magnesium Binding Sites List in 5vzf
Magnesium binding site 2 out of 4 in the Post-Catalytic Complex of Human Polymerase Mu (W434A) Mutant with Incoming Dttp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Post-Catalytic Complex of Human Polymerase Mu (W434A) Mutant with Incoming Dttp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg703

b:2.3
occ:0.44
 NA A:NA705 0.0 22.0 0.6
OD2 A:ASP330 2.0 23.0 1.0
OD1 A:ASP332 2.1 9.2 1.0
OD2 A:ASP418 2.1 14.5 1.0
O P:HOH818 2.2 9.7 0.4
O A:HOH864 2.3 13.4 0.4
OP1 P:DT5 2.3 6.4 0.6
O3' P:DA4 2.3 6.9 0.6
O2A P:TTP701 2.3 3.6 0.4
CG A:ASP330 2.8 17.8 1.0
P P:DT5 2.9 6.0 0.6
OD1 A:ASP330 3.1 8.6 1.0
CG A:ASP332 3.1 7.8 1.0
CG A:ASP418 3.3 13.9 1.0
OD2 A:ASP332 3.4 6.6 1.0
PA P:TTP701 3.4 7.2 0.4
MG A:MG702 3.5 7.1 1.0
C3' P:DA4 3.5 6.6 0.6
C4' P:DA4 3.6 9.6 0.6
C5' P:DA4 3.7 9.6 0.6
CB A:ASP418 3.9 7.3 1.0
O1A P:TTP701 3.9 8.2 0.4
O5' P:TTP701 4.0 1.7 0.4
OP2 P:DT5 4.0 6.3 0.6
O P:HOH819 4.0 20.1 0.6
O5' P:DT5 4.1 9.8 0.6
CB A:ASP330 4.2 8.9 1.0
C5' P:DT5 4.2 10.0 0.6
C5' P:TTP701 4.2 3.3 0.4
OD1 A:ASP418 4.3 12.5 1.0
O A:HOH1042 4.3 21.7 1.0
CB A:ASP332 4.4 6.2 1.0
CE1 A:HIS329 4.4 18.6 0.4
O5' P:DA4 4.6 8.2 0.6
C2' P:DA4 4.6 6.7 0.6
OP1 P:DA4 4.6 13.6 0.4
NH2 A:ARG416 4.6 12.1 1.0
O2B A:TTP701 4.6 9.3 0.6
O3G P:TTP701 4.7 6.3 0.4
O2B P:TTP701 4.9 4.2 0.4
O3A P:TTP701 4.9 5.3 0.4
OP1 P:DA4 4.9 11.5 0.6
O A:VAL331 5.0 6.8 1.0
CA A:ASP332 5.0 7.0 1.0

Magnesium binding site 3 out of 4 in 5vzf

Go back to Magnesium Binding Sites List in 5vzf
Magnesium binding site 3 out of 4 in the Post-Catalytic Complex of Human Polymerase Mu (W434A) Mutant with Incoming Dttp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Post-Catalytic Complex of Human Polymerase Mu (W434A) Mutant with Incoming Dttp within 5.0Å range:
probe atom residue distance (Å) B Occ
T:Mg101

b:20.3
occ:0.49
 O T:HOH207 1.9 26.1 1.0
O T:HOH214 2.1 42.5 1.0
O T:HOH219 2.1 34.1 1.0
O T:HOH237 2.1 42.7 1.0
N7 T:DG2 4.2 22.2 1.0
O6 T:DG3 4.2 18.1 1.0
O6 T:DG2 4.2 18.7 1.0
N4 D:DC2 4.3 17.7 1.0
O T:HOH205 4.3 34.8 1.0
O T:HOH211 4.5 27.9 1.0
O T:HOH240 4.6 43.4 1.0
C5 T:DG2 4.9 19.8 1.0
C6 T:DG2 5.0 18.5 1.0

Magnesium binding site 4 out of 4 in 5vzf

Go back to Magnesium Binding Sites List in 5vzf
Magnesium binding site 4 out of 4 in the Post-Catalytic Complex of Human Polymerase Mu (W434A) Mutant with Incoming Dttp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Post-Catalytic Complex of Human Polymerase Mu (W434A) Mutant with Incoming Dttp within 5.0Å range:
probe atom residue distance (Å) B Occ
P:Mg702

b:12.3
occ:0.56
 O1A P:TTP701 1.7 8.2 0.4
O1B A:TTP701 1.9 13.6 0.6
O A:HOH906 2.0 13.2 0.6
O A:HOH823 2.0 19.3 0.6
OP2 P:DT5 2.1 6.3 0.6
O P:HOH815 2.1 10.8 0.6
O P:HOH819 2.1 20.1 0.6
PA P:TTP701 3.1 7.2 0.4
C5' P:DA4 3.3 15.0 0.4
CE1 A:HIS329 3.3 18.6 0.4
PB A:TTP701 3.3 12.9 0.6
P P:DT5 3.4 6.0 0.6
O3A P:TTP701 3.6 5.3 0.4
O P:HOH809 3.7 19.3 1.0
O P:HOH818 3.8 9.7 0.4
O3B A:TTP701 3.9 6.8 0.6
C7 P:DT5 3.9 16.2 0.6
ND1 A:HIS329 4.0 16.8 0.4
OP1 P:DT5 4.0 6.4 0.6
O2A P:TTP701 4.0 3.6 0.4
C5M P:TTP701 4.1 8.3 0.4
NE2 A:HIS329 4.1 13.7 0.4
C4' P:DA4 4.1 17.1 0.4
OP1 P:DA4 4.1 13.6 0.4
O5' A:TTP701 4.2 34.2 0.6
O2B A:TTP701 4.2 9.3 0.6
O5' P:TTP701 4.2 1.7 0.4
O3' P:DA4 4.3 6.9 0.6
O1G P:TTP701 4.3 16.9 0.4
O5' P:DA4 4.3 10.2 0.4
O P:HOH825 4.3 19.7 0.6
O4' P:DA4 4.4 16.9 0.4
O3A A:TTP701 4.4 16.9 0.6
O5' P:DT5 4.4 9.8 0.6
O5' P:DA4 4.5 8.2 0.6
OP2 P:DA4 4.5 13.2 0.6
OP1 P:DA4 4.5 11.5 0.6
C3' P:DA4 4.5 6.6 0.6
O3G P:TTP701 4.6 6.3 0.4
P P:DA4 4.7 8.8 0.6
PA A:TTP701 4.7 30.7 0.6
O1A A:TTP701 4.8 29.0 0.6
P P:DA4 4.9 11.8 0.4
OD2 A:ASP330 4.9 23.0 1.0
PG P:TTP701 4.9 10.3 0.4

Reference:

A.F.Moon, J.M.Pryor, D.A.Ramsden, T.A.Kunkel, K.Bebenek, L.C.Pedersen. Structural Accommodation of Ribonucleotide Incorporation By the Dna Repair Enzyme Polymerase Mu. Nucleic Acids Res. V. 45 9138 2017.
ISSN: ESSN 1362-4962
PubMed: 28911097
DOI: 10.1093/NAR/GKX527
Page generated: Mon Sep 30 06:24:14 2024

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