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Magnesium in PDB 5vzi: Post-Catalytic Complex of Human Polymerase Mu (W434H) Mutant with Incoming Dttp

Enzymatic activity of Post-Catalytic Complex of Human Polymerase Mu (W434H) Mutant with Incoming Dttp

All present enzymatic activity of Post-Catalytic Complex of Human Polymerase Mu (W434H) Mutant with Incoming Dttp:
2.7.7.7;

Protein crystallography data

The structure of Post-Catalytic Complex of Human Polymerase Mu (W434H) Mutant with Incoming Dttp, PDB code: 5vzi 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) 32.88 / 1.50
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 60.132, 68.838, 111.023, 90.00, 90.00, 90.00
R / Rfree (%) 17.1 / 19.4

Other elements in 5vzi:

The structure of Post-Catalytic Complex of Human Polymerase Mu (W434H) 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 (W434H) Mutant with Incoming Dttp (pdb code 5vzi). 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 (W434H) Mutant with Incoming Dttp, PDB code: 5vzi:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 5vzi

Go back to Magnesium Binding Sites List in 5vzi
Magnesium binding site 1 out of 4 in the Post-Catalytic Complex of Human Polymerase Mu (W434H) 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 (W434H) Mutant with Incoming Dttp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg703

b:9.2
occ:1.00
 O2A A:TTP702 2.0 7.7 0.6
O2B A:TTP702 2.0 4.8 0.6
OD2 A:ASP332 2.1 6.3 1.0
OD1 A:ASP330 2.1 8.5 1.0
O A:HOH887 2.1 9.0 1.0
O2B A:TTP701 2.1 8.3 0.4
O2G A:TTP701 2.2 6.0 0.4
O3G A:TTP702 2.2 9.1 0.6
OP1 P:DT5 2.3 9.6 0.4
PB A:TTP702 3.0 8.8 0.6
PA A:TTP702 3.1 6.8 0.6
CG A:ASP332 3.1 7.5 1.0
CG A:ASP330 3.2 16.6 1.0
O3A A:TTP702 3.2 5.6 0.6
PG A:TTP701 3.3 8.8 0.4
PG A:TTP702 3.3 9.2 0.6
PB A:TTP701 3.4 14.8 0.4
OD1 A:ASP332 3.5 10.7 1.0
O3B A:TTP702 3.5 5.3 0.6
MG A:MG704 3.5 9.2 0.4
NA A:NA706 3.5 9.0 0.6
O3B A:TTP701 3.6 9.4 0.4
OD2 A:ASP330 3.6 15.7 1.0
P P:DT5 3.7 9.4 0.4
O A:ASP330 4.0 7.9 1.0
O5' A:TTP702 4.1 5.9 0.6
C5' A:TTP702 4.1 6.5 0.6
O2G A:TTP702 4.1 14.4 0.6
O3G A:TTP701 4.1 10.2 0.4
ND1 A:HIS329 4.2 14.2 0.6
O A:HOH853 4.2 9.1 1.0
O A:HOH816 4.2 18.6 1.0
C5' P:DT5 4.2 15.0 0.4
O1A A:TTP702 4.2 8.6 0.6
O5' P:DT5 4.3 12.6 0.4
O1B A:TTP702 4.3 8.2 0.6
O1B A:TTP701 4.3 16.8 0.4
N A:GLY320 4.3 6.1 1.0
C A:ASP330 4.3 7.8 1.0
CE1 A:HIS329 4.3 10.2 0.6
CB A:ASP332 4.4 7.2 1.0
O1G A:TTP702 4.5 16.2 0.6
CB A:ASP330 4.5 10.1 1.0
O1G A:TTP701 4.5 9.1 0.4
O3' P:DA4 4.6 9.4 0.4
OP2 P:DT5 4.6 9.4 0.4
O3A A:TTP701 4.6 17.7 0.4
N A:ASP330 4.7 9.2 1.0
CA A:GLY319 4.7 5.7 1.0
CA A:ASP330 4.7 9.2 1.0
O P:HOH209 4.8 8.5 0.6
N A:ASP332 4.8 6.8 1.0
O A:HOH921 4.8 12.7 0.6
N A:VAL331 4.9 7.6 1.0

Magnesium binding site 2 out of 4 in 5vzi

Go back to Magnesium Binding Sites List in 5vzi
Magnesium binding site 2 out of 4 in the Post-Catalytic Complex of Human Polymerase Mu (W434H) 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 (W434H) Mutant with Incoming Dttp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg704

b:9.2
occ:0.42
 NA A:NA706 0.0 9.0 0.6
OD2 A:ASP330 1.9 15.7 1.0
OD1 A:ASP332 2.1 10.7 1.0
OD2 A:ASP418 2.1 12.5 1.0
O P:HOH209 2.1 8.5 0.6
O A:HOH921 2.2 12.7 0.6
OP1 P:DT5 2.3 9.6 0.4
O3' P:DA4 2.3 9.4 0.4
O2A A:TTP702 2.4 7.7 0.6
CG A:ASP330 2.9 16.6 1.0
P P:DT5 2.9 9.4 0.4
CG A:ASP332 3.1 7.5 1.0
OD1 A:ASP330 3.1 8.5 1.0
CG A:ASP418 3.2 13.0 1.0
OD2 A:ASP332 3.4 6.3 1.0
PA A:TTP702 3.4 6.8 0.6
C3' P:DA4 3.5 11.1 0.4
MG A:MG703 3.5 9.2 1.0
C4' P:DA4 3.6 9.9 0.4
C5' P:DA4 3.6 12.4 0.4
CB A:ASP418 3.8 10.1 1.0
O5' A:TTP702 3.9 5.9 0.6
O1A A:TTP702 4.0 8.6 0.6
OP2 P:DT5 4.0 9.4 0.4
O P:HOH207 4.0 14.7 0.4
O5' P:DT5 4.1 12.6 0.4
CE1 A:HIS329 4.1 10.2 0.6
C5' A:TTP702 4.2 6.5 0.6
C5' P:DT5 4.2 15.0 0.4
CB A:ASP330 4.2 10.1 1.0
OD1 A:ASP418 4.3 12.3 1.0
O A:HOH1019 4.3 19.0 1.0
O5' P:DA4 4.4 13.8 0.4
CB A:ASP332 4.4 7.2 1.0
OP1 P:DA4 4.4 11.9 0.6
C2' P:DA4 4.6 9.4 0.4
NH2 A:ARG416 4.6 13.7 1.0
O2B A:TTP701 4.6 8.3 0.4
O3A A:TTP702 4.8 5.6 0.6
OP1 P:DA4 4.8 13.4 0.4
O3G A:TTP702 4.9 9.1 0.6
NE2 A:HIS329 4.9 9.0 0.6
O2G A:TTP701 5.0 6.0 0.4
ND1 A:HIS329 5.0 14.2 0.6
O4' P:DA4 5.0 11.0 0.4

Magnesium binding site 3 out of 4 in 5vzi

Go back to Magnesium Binding Sites List in 5vzi
Magnesium binding site 3 out of 4 in the Post-Catalytic Complex of Human Polymerase Mu (W434H) 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 (W434H) Mutant with Incoming Dttp within 5.0Å range:
probe atom residue distance (Å) B Occ
T:Mg101

b:28.0
occ:0.59
 O T:HOH220 2.0 29.0 1.0
O T:HOH217 2.1 37.0 1.0
O T:HOH224 2.2 38.6 1.0
O T:HOH240 2.2 50.7 1.0
O D:HOH121 4.1 49.8 1.0
N7 T:DG2 4.1 23.4 1.0
O6 T:DG3 4.2 18.6 1.0
O T:HOH207 4.4 28.3 1.0
O6 T:DG2 4.4 20.0 1.0
N4 D:DC2 4.4 19.6 1.0
O T:HOH202 4.5 40.9 1.0
C5 T:DG2 4.9 21.4 1.0

Magnesium binding site 4 out of 4 in 5vzi

Go back to Magnesium Binding Sites List in 5vzi
Magnesium binding site 4 out of 4 in the Post-Catalytic Complex of Human Polymerase Mu (W434H) 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 (W434H) Mutant with Incoming Dttp within 5.0Å range:
probe atom residue distance (Å) B Occ
P:Mg101

b:13.6
occ:0.42
 O1A A:TTP702 1.7 8.6 0.6
OP2 P:DT5 2.0 9.4 0.4
O1B A:TTP701 2.0 16.8 0.4
O P:HOH207 2.0 14.7 0.4
O A:HOH822 2.0 25.1 0.4
O P:HOH211 2.1 13.9 0.4
PA A:TTP702 3.1 6.8 0.6
CE1 A:HIS329 3.2 10.2 0.6
C5' P:DA4 3.2 14.3 0.6
O3' P:DT5 3.3 36.8 0.6
P P:DT5 3.3 9.4 0.4
PB A:TTP701 3.4 14.8 0.4
O3A A:TTP702 3.6 5.6 0.6
O P:HOH209 3.7 8.5 0.6
NE2 A:HIS329 3.8 9.0 0.6
O A:HOH985 3.8 25.0 1.0
ND1 A:HIS329 3.8 14.2 0.6
OP1 P:DT5 3.9 9.6 0.4
C5M A:TTP702 3.9 13.8 0.6
C7 P:DT5 3.9 21.0 0.4
C3' P:DT5 4.0 28.5 0.6
O2A A:TTP702 4.0 7.7 0.6
O3B A:TTP701 4.0 9.4 0.4
OP1 P:DA4 4.0 11.9 0.6
O5' P:DA4 4.0 10.3 0.6
C4' P:DA4 4.1 15.3 0.6
O P:HOH225 4.1 18.4 0.4
O5' P:DA4 4.2 13.8 0.4
O2B A:TTP701 4.2 8.3 0.4
O3' P:DA4 4.2 9.4 0.4
O4' P:DA4 4.2 15.8 0.6
O5' A:TTP702 4.3 5.9 0.6
O1G A:TTP702 4.4 16.2 0.6
O5' P:DT5 4.4 12.6 0.4
OP2 P:DA4 4.4 14.9 0.4
OP1 P:DA4 4.4 13.4 0.4
C2' P:DT5 4.4 29.5 0.6
O3A A:TTP701 4.4 17.7 0.4
C3' P:DA4 4.5 11.1 0.4
P P:DA4 4.5 13.5 0.4
CD2 A:HIS329 4.7 9.2 0.6
P P:DA4 4.7 10.6 0.6
CG A:HIS329 4.7 10.6 0.6
O3G A:TTP702 4.7 9.1 0.6
O A:HOH810 4.8 36.6 1.0

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 06:25:16 2024

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