Magnesium in PDB 5t14: Dna Polymerase Kappa Extending Beyond A Bulky Major Benzo[A]Pyrene Adduct

Enzymatic activity of Dna Polymerase Kappa Extending Beyond A Bulky Major Benzo[A]Pyrene Adduct

All present enzymatic activity of Dna Polymerase Kappa Extending Beyond A Bulky Major Benzo[A]Pyrene Adduct:
2.7.7.7;

Protein crystallography data

The structure of Dna Polymerase Kappa Extending Beyond A Bulky Major Benzo[A]Pyrene Adduct, PDB code: 5t14 was solved by V.K.Jha, H.Ling, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 40.00 / 3.00
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 65.250, 128.820, 167.460, 90.00, 90.00, 90.00
R / Rfree (%) 20.4 / 26.6

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Dna Polymerase Kappa Extending Beyond A Bulky Major Benzo[A]Pyrene Adduct (pdb code 5t14). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Dna Polymerase Kappa Extending Beyond A Bulky Major Benzo[A]Pyrene Adduct, PDB code: 5t14:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 5t14

Go back to Magnesium Binding Sites List in 5t14
Magnesium binding site 1 out of 4 in the Dna Polymerase Kappa Extending Beyond A Bulky Major Benzo[A]Pyrene Adduct


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Dna Polymerase Kappa Extending Beyond A Bulky Major Benzo[A]Pyrene Adduct within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg601

b:47.1
occ:1.00
 O1A A:DZ4603 2.2 47.6 1.0
OD1 A:ASP107 2.2 50.2 1.0
O1B A:DZ4603 2.2 53.4 1.0
O3G A:DZ4603 2.2 52.2 1.0
OD2 A:ASP198 2.2 59.6 1.0
O A:MET108 2.2 54.8 1.0
PB A:DZ4603 3.3 55.0 1.0
CG A:ASP107 3.3 53.4 1.0
C A:MET108 3.4 55.9 1.0
PA A:DZ4603 3.4 55.8 1.0
CG A:ASP198 3.4 64.3 1.0
PG A:DZ4603 3.5 52.7 1.0
N3A A:DZ4603 3.7 56.9 1.0
NZ A:LYS328 3.7 71.8 1.0
O3B A:DZ4603 3.8 52.4 1.0
OD2 A:ASP107 3.9 53.5 1.0
N A:MET108 3.9 55.3 1.0
C5' A:DZ4603 4.1 57.8 1.0
OD1 A:ASP198 4.1 68.4 1.0
CA A:MET108 4.2 55.9 1.0
O1G A:DZ4603 4.2 55.3 1.0
O5' A:DZ4603 4.2 57.1 1.0
OE2 A:GLU199 4.3 58.5 1.0
C A:ASP107 4.3 55.5 1.0
N A:ASP109 4.4 52.2 1.0
CB A:ASP198 4.5 62.7 1.0
CB A:ASP107 4.6 52.9 1.0
O2G A:DZ4603 4.6 52.6 1.0
O2A A:DZ4603 4.6 53.7 1.0
CB A:MET108 4.7 56.5 1.0
CE A:LYS328 4.7 72.4 1.0
O2B A:DZ4603 4.7 49.6 1.0
CA A:ASP109 4.7 51.1 1.0
CA A:ASP107 4.7 53.9 1.0
N A:ALA110 4.8 46.8 1.0
O A:ASP107 4.8 61.8 1.0
CB A:PHE111 4.9 53.9 1.0
C A:ASP109 4.9 48.3 1.0
CD A:GLU199 5.0 63.2 1.0
CG A:GLU199 5.0 62.3 1.0
N A:PHE111 5.0 53.5 1.0

Magnesium binding site 2 out of 4 in 5t14

Go back to Magnesium Binding Sites List in 5t14
Magnesium binding site 2 out of 4 in the Dna Polymerase Kappa Extending Beyond A Bulky Major Benzo[A]Pyrene Adduct


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Dna Polymerase Kappa Extending Beyond A Bulky Major Benzo[A]Pyrene Adduct within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg602

b:66.3
occ:1.00
 O A:HOH721 2.2 54.2 1.0
O A:ILE357 2.2 57.0 1.0
O A:VAL354 2.2 62.9 1.0
OP1 C:DA12 2.2 62.0 1.0
O A:ARG352 2.2 77.6 1.0
C A:VAL354 3.3 64.5 1.0
C A:ILE357 3.3 52.7 1.0
C A:ARG352 3.4 77.3 1.0
P C:DA12 3.6 60.9 1.0
N A:ILE357 3.9 58.1 1.0
CA A:SER355 4.0 63.8 1.0
N A:SER355 4.0 65.2 1.0
N A:GLY356 4.0 59.4 1.0
CA A:ILE357 4.1 55.0 1.0
N A:VAL354 4.1 66.4 1.0
C A:LYS353 4.2 71.9 1.0
OP2 C:DA12 4.2 60.3 1.0
N A:GLY358 4.3 51.7 1.0
CA A:VAL354 4.3 65.2 1.0
CA A:ARG352 4.3 76.2 1.0
C A:SER355 4.3 62.9 1.0
N A:LYS353 4.4 76.4 1.0
NH2 A:ARG352 4.4 76.2 1.0
CB A:ILE357 4.4 55.8 1.0
CA A:GLY358 4.4 54.6 1.0
CA A:LYS353 4.5 76.6 1.0
O5' C:DA12 4.5 62.1 1.0
O A:LYS353 4.6 72.5 1.0
O3' C:DG11 4.6 61.2 1.0
CD A:ARG352 4.7 75.7 1.0
C A:GLY356 4.7 59.9 1.0
O A:ILE351 4.7 74.9 1.0
O A:HOH706 4.8 57.0 1.0
CG A:ARG352 4.9 76.0 1.0
CA A:GLY356 4.9 59.4 1.0

Magnesium binding site 3 out of 4 in 5t14

Go back to Magnesium Binding Sites List in 5t14
Magnesium binding site 3 out of 4 in the Dna Polymerase Kappa Extending Beyond A Bulky Major Benzo[A]Pyrene Adduct


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Dna Polymerase Kappa Extending Beyond A Bulky Major Benzo[A]Pyrene Adduct within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg602

b:65.2
occ:1.00
 O3G B:DZ4604 2.2 62.0 1.0
O2A B:DZ4604 2.2 69.7 1.0
OD1 B:ASP107 2.2 76.3 1.0
O2B B:DZ4604 2.2 60.2 1.0
OD2 B:ASP198 2.2 75.3 1.0
O B:MET108 2.2 71.8 1.0
PB B:DZ4604 3.2 65.1 1.0
CG B:ASP107 3.3 80.0 1.0
CG B:ASP198 3.3 77.7 1.0
C B:MET108 3.3 67.7 1.0
PA B:DZ4604 3.4 71.0 1.0
PG B:DZ4604 3.4 63.9 1.0
N3A B:DZ4604 3.6 67.0 1.0
NZ B:LYS328 3.7 0.8 1.0
O3B B:DZ4604 3.7 64.6 1.0
OD2 B:ASP107 3.8 81.6 1.0
OD1 B:ASP198 3.8 77.5 1.0
N B:MET108 3.9 70.4 1.0
C B:ASP107 4.1 71.8 1.0
CA B:MET108 4.1 70.6 1.0
O2G B:DZ4604 4.1 66.7 1.0
C5' B:DZ4604 4.3 66.8 1.0
O5' B:DZ4604 4.4 67.6 1.0
N B:ASP109 4.4 65.8 1.0
O B:ASP107 4.4 69.0 1.0
CB B:ASP198 4.4 78.0 1.0
O B:HOH709 4.5 50.0 1.0
O1A B:DZ4604 4.5 75.2 1.0
CB B:ASP107 4.5 77.9 1.0
O1G B:DZ4604 4.5 66.6 1.0
CB B:MET108 4.6 72.0 1.0
CA B:ASP109 4.6 70.0 1.0
O1B B:DZ4604 4.7 61.8 1.0
CA B:ASP107 4.7 73.7 1.0
N B:ALA110 4.7 73.8 1.0
CE B:LYS328 4.8 0.9 1.0
N B:PHE111 4.9 72.3 1.0
C B:ASP109 4.9 71.1 1.0
CB B:PHE111 5.0 70.0 1.0

Magnesium binding site 4 out of 4 in 5t14

Go back to Magnesium Binding Sites List in 5t14
Magnesium binding site 4 out of 4 in the Dna Polymerase Kappa Extending Beyond A Bulky Major Benzo[A]Pyrene Adduct


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Dna Polymerase Kappa Extending Beyond A Bulky Major Benzo[A]Pyrene Adduct within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg603

b:73.5
occ:1.00
 O B:ILE357 2.2 66.8 1.0
O B:VAL354 2.2 68.4 1.0
OP1 P:DA12 2.2 66.9 1.0
O B:ARG352 2.2 81.1 1.0
C B:VAL354 3.3 69.1 1.0
C B:ILE357 3.3 62.1 1.0
C B:ARG352 3.5 75.0 1.0
P P:DA12 3.6 63.4 1.0
N B:ILE357 3.8 68.2 1.0
N B:GLY356 3.9 71.2 1.0
CA B:SER355 3.9 71.0 1.0
CA B:ILE357 4.0 64.6 1.0
N B:SER355 4.0 69.4 1.0
N B:VAL354 4.2 66.9 1.0
C B:LYS353 4.3 71.9 1.0
OP2 P:DA12 4.3 59.4 1.0
CB B:ILE357 4.3 64.6 1.0
C B:SER355 4.4 70.7 1.0
NH2 B:ARG352 4.4 83.1 1.0
N B:GLY358 4.4 60.4 1.0
CA B:ARG352 4.4 76.2 1.0
CA B:VAL354 4.4 68.8 1.0
N B:LYS353 4.4 75.1 1.0
O3' P:DG11 4.5 63.1 1.0
CA B:LYS353 4.6 76.3 1.0
CA B:GLY358 4.6 62.3 1.0
O B:LYS353 4.7 68.1 1.0
C B:GLY356 4.7 70.3 1.0
O5' P:DA12 4.7 65.0 1.0
CD B:ARG352 4.7 82.9 1.0
O B:ILE351 4.9 73.0 1.0
CA B:GLY356 4.9 70.5 1.0
CG B:ARG352 4.9 84.0 1.0

Reference:

V.Jha, H.Ling. Structural Basis of Accurate Replication Beyond A Bulky Major Benzo[A]Pyrene Adduct By Human Dna Polymerase Kappa. Dna Repair (Amst.) V. 49 43 2017.
ISSN: ISSN 1568-7856
PubMed: 27894903
DOI: 10.1016/J.DNAREP.2016.11.001
Page generated: Mon Dec 14 21:11:06 2020

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