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Magnesium in PDB 4u6p: Structural Mechanism of Error-Free Bypass of Major Benzo[A]Pyrene Adduct By Human Polymerase Kappa

Enzymatic activity of Structural Mechanism of Error-Free Bypass of Major Benzo[A]Pyrene Adduct By Human Polymerase Kappa

All present enzymatic activity of Structural Mechanism of Error-Free Bypass of Major Benzo[A]Pyrene Adduct By Human Polymerase Kappa:
2.7.7.7;

Protein crystallography data

The structure of Structural Mechanism of Error-Free Bypass of Major Benzo[A]Pyrene Adduct By Human Polymerase Kappa, PDB code: 4u6p 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) 46.23 / 2.59
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 66.150, 129.286, 167.713, 90.00, 90.00, 90.00
R / Rfree (%) 20 / 23.9

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Structural Mechanism of Error-Free Bypass of Major Benzo[A]Pyrene Adduct By Human Polymerase Kappa (pdb code 4u6p). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the Structural Mechanism of Error-Free Bypass of Major Benzo[A]Pyrene Adduct By Human Polymerase Kappa, PDB code: 4u6p:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in 4u6p

Go back to Magnesium Binding Sites List in 4u6p
Magnesium binding site 1 out of 6 in the Structural Mechanism of Error-Free Bypass of Major Benzo[A]Pyrene Adduct By Human Polymerase Kappa


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structural Mechanism of Error-Free Bypass of Major Benzo[A]Pyrene Adduct By Human Polymerase Kappa within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg601

b:22.0
occ:1.00
 O C:HOH103 2.4 35.0 1.0
O A:VAL354 2.5 36.8 1.0
O A:HOH713 2.6 45.4 1.0
OP1 C:DA12 2.7 41.0 1.0
O A:ILE357 2.7 40.1 1.0
O A:ARG352 2.7 38.7 1.0
C A:VAL354 3.5 43.2 1.0
C A:ILE357 3.6 42.7 1.0
NH2 A:ARG352 3.7 51.9 1.0
P C:DA12 3.8 37.0 1.0
C A:ARG352 3.8 45.3 1.0
N A:ILE357 4.0 43.6 1.0
OP2 C:DA12 4.0 33.0 1.0
C A:LYS353 4.1 41.0 1.0
O A:LYS353 4.1 42.3 1.0
N A:VAL354 4.1 37.3 1.0
N A:SER355 4.2 39.9 1.0
CA A:SER355 4.2 51.6 1.0
N A:GLY356 4.2 46.0 1.0
CA A:ILE357 4.3 40.4 1.0
CA A:VAL354 4.4 35.9 1.0
CB A:ILE357 4.5 43.2 1.0
CA A:LYS353 4.6 42.6 1.0
N A:GLY358 4.6 45.1 1.0
C A:SER355 4.6 44.5 1.0
N A:LYS353 4.6 42.1 1.0
CD A:ARG352 4.7 46.5 1.0
CA A:ARG352 4.7 38.1 1.0
O3' C:DC11 4.8 35.8 1.0
CA A:GLY358 4.9 31.8 1.0
O5' C:DA12 4.9 30.9 1.0
C A:GLY356 4.9 46.0 1.0
CZ A:ARG352 4.9 39.5 1.0

Magnesium binding site 2 out of 6 in 4u6p

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Magnesium binding site 2 out of 6 in the Structural Mechanism of Error-Free Bypass of Major Benzo[A]Pyrene Adduct By Human Polymerase Kappa


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structural Mechanism of Error-Free Bypass of Major Benzo[A]Pyrene Adduct By Human Polymerase Kappa within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg602

b:49.7
occ:1.00
 OD1 A:ASP107 2.0 64.4 1.0
O2B A:DCT604 2.1 55.6 1.0
OD2 A:ASP198 2.5 57.9 1.0
O1G A:DCT604 2.5 57.0 1.0
O A:MET108 2.7 42.4 1.0
MG A:MG603 2.7 65.1 1.0
CG A:ASP107 3.1 64.0 1.0
PB A:DCT604 3.4 69.6 1.0
PG A:DCT604 3.6 59.5 1.0
O3B A:DCT604 3.6 66.1 1.0
OD2 A:ASP107 3.7 60.5 1.0
CG A:ASP198 3.7 52.3 1.0
C A:MET108 3.9 38.6 1.0
O2A A:DCT604 3.9 65.3 1.0
NZ A:LYS328 4.0 58.6 1.0
O3G A:DCT604 4.0 53.3 1.0
O3A A:DCT604 4.2 59.8 1.0
C5' A:DCT604 4.3 51.9 1.0
N A:MET108 4.3 38.2 1.0
CB A:ASP107 4.4 40.8 1.0
OD1 A:ASP198 4.4 50.3 1.0
OE2 A:GLU199 4.5 52.4 1.0
N A:ALA110 4.5 37.2 1.0
C A:ASP107 4.5 41.8 1.0
O1B A:DCT604 4.6 58.4 1.0
PA A:DCT604 4.6 76.5 1.0
CA A:MET108 4.7 30.8 1.0
CA A:ASP107 4.8 40.4 1.0
CB A:ASP198 4.8 43.3 1.0
O5' A:DCT604 4.8 45.1 1.0
N A:ASP109 4.8 31.9 1.0
CA A:ASP109 4.8 34.6 1.0
CG A:GLU199 4.8 52.2 1.0
O2G A:DCT604 4.9 65.1 1.0
N A:PHE111 4.9 37.0 1.0

Magnesium binding site 3 out of 6 in 4u6p

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Magnesium binding site 3 out of 6 in the Structural Mechanism of Error-Free Bypass of Major Benzo[A]Pyrene Adduct By Human Polymerase Kappa


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Structural Mechanism of Error-Free Bypass of Major Benzo[A]Pyrene Adduct By Human Polymerase Kappa within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg603

b:65.1
occ:1.00
 OE2 A:GLU199 2.0 52.4 1.0
O2A A:DCT604 2.6 65.3 1.0
MG A:MG602 2.7 49.7 1.0
O A:HOH745 3.0 48.5 1.0
CD A:GLU199 3.0 55.4 1.0
OD2 A:ASP107 3.2 60.5 1.0
OD1 A:ASP107 3.2 64.4 1.0
O2B A:DCT604 3.4 55.6 1.0
CG A:GLU199 3.5 52.2 1.0
OD2 A:ASP198 3.5 57.9 1.0
CG A:ASP107 3.5 64.0 1.0
C5' A:DCT604 3.5 51.9 1.0
O1G A:DCT604 3.6 57.0 1.0
PA A:DCT604 3.9 76.5 1.0
OE1 A:GLU199 4.1 43.1 1.0
O A:HOH735 4.1 56.0 1.0
O5' A:DCT604 4.2 45.1 1.0
OD1 A:ASP198 4.2 50.3 1.0
CG A:ASP198 4.2 52.3 1.0
O3A A:DCT604 4.5 59.8 1.0
PB A:DCT604 4.6 69.6 1.0
CB A:GLU199 4.7 41.8 1.0
C4' A:DCT604 4.8 55.0 1.0
C3' C:DC13 4.9 39.2 1.0

Magnesium binding site 4 out of 6 in 4u6p

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Magnesium binding site 4 out of 6 in the Structural Mechanism of Error-Free Bypass of Major Benzo[A]Pyrene Adduct By Human Polymerase Kappa


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Structural Mechanism of Error-Free Bypass of Major Benzo[A]Pyrene Adduct By Human Polymerase Kappa within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg602

b:34.7
occ:1.00
 O B:VAL354 2.5 49.2 1.0
O B:ARG352 2.7 49.6 1.0
OP1 P:DA12 2.8 46.5 1.0
O B:ILE357 2.8 41.6 1.0
C B:VAL354 3.5 52.4 1.0
NH2 B:ARG352 3.6 60.5 1.0
OP2 P:DA12 3.7 30.3 1.0
P P:DA12 3.7 44.6 1.0
C B:ILE357 3.8 42.9 1.0
C B:ARG352 3.8 46.9 1.0
N B:ILE357 4.1 37.5 1.0
N B:VAL354 4.2 39.7 1.0
C B:LYS353 4.2 39.4 1.0
N B:SER355 4.3 50.2 1.0
CA B:SER355 4.3 46.5 1.0
N B:GLY356 4.3 45.7 1.0
CA B:ILE357 4.4 41.1 1.0
O B:LYS353 4.5 50.1 1.0
CA B:VAL354 4.5 43.5 1.0
CB B:ILE357 4.6 50.2 1.0
CD B:ARG352 4.6 60.1 1.0
N B:LYS353 4.7 41.4 1.0
CA B:LYS353 4.7 41.6 1.0
CA B:ARG352 4.7 43.7 1.0
N B:GLY358 4.7 47.6 1.0
C B:SER355 4.7 48.1 1.0
O3' P:DC11 4.8 40.1 1.0
CZ B:ARG352 4.8 65.0 1.0
O5' P:DA12 4.8 34.2 1.0
CA B:GLY358 4.9 42.2 1.0
O B:ILE351 5.0 48.4 1.0

Magnesium binding site 5 out of 6 in 4u6p

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Magnesium binding site 5 out of 6 in the Structural Mechanism of Error-Free Bypass of Major Benzo[A]Pyrene Adduct By Human Polymerase Kappa


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Structural Mechanism of Error-Free Bypass of Major Benzo[A]Pyrene Adduct By Human Polymerase Kappa within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg603

b:56.1
occ:1.00
 O3G B:DCT605 1.9 68.4 1.0
OD1 B:ASP107 2.0 74.0 1.0
O2B B:DCT605 2.2 65.2 1.0
OD2 B:ASP198 2.9 70.5 1.0
MG B:MG604 2.9 75.6 1.0
O B:MET108 2.9 61.2 1.0
CG B:ASP107 3.1 75.7 1.0
O2A B:DCT605 3.2 67.2 1.0
PG B:DCT605 3.3 61.1 1.0
PB B:DCT605 3.4 71.1 1.0
OD2 B:ASP107 3.5 70.8 1.0
O3B B:DCT605 3.5 65.1 1.0
NZ B:LYS328 4.0 67.5 1.0
O3A B:DCT605 4.0 82.5 1.0
CG B:ASP198 4.1 63.9 1.0
O1G B:DCT605 4.1 64.7 1.0
C B:MET108 4.1 49.2 1.0
PA B:DCT605 4.3 85.4 1.0
CB B:ASP107 4.3 60.2 1.0
O2G B:DCT605 4.4 62.9 1.0
N B:MET108 4.6 56.5 1.0
N B:ALA110 4.7 45.8 1.0
OD1 B:ASP198 4.7 72.5 1.0
O1B B:DCT605 4.7 64.0 1.0
C B:ASP107 4.7 61.3 1.0
CE B:LYS328 4.8 70.2 1.0
OE2 B:GLU199 4.8 73.2 1.0
CA B:ASP107 4.9 50.5 1.0
O B:HOH722 4.9 58.9 1.0
CA B:MET108 5.0 45.8 1.0
O5' B:DCT605 5.0 62.3 1.0

Magnesium binding site 6 out of 6 in 4u6p

Go back to Magnesium Binding Sites List in 4u6p
Magnesium binding site 6 out of 6 in the Structural Mechanism of Error-Free Bypass of Major Benzo[A]Pyrene Adduct By Human Polymerase Kappa


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Structural Mechanism of Error-Free Bypass of Major Benzo[A]Pyrene Adduct By Human Polymerase Kappa within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg604

b:75.6
occ:1.00
 OE2 B:GLU199 2.1 73.2 1.0
O2A B:DCT605 2.5 67.2 1.0
MG B:MG603 2.9 56.1 1.0
O B:HOH722 3.0 58.9 1.0
CD B:GLU199 3.1 75.1 1.0
OD2 B:ASP107 3.2 70.8 1.0
OD1 B:ASP107 3.4 74.0 1.0
CG B:GLU199 3.5 64.3 1.0
CG B:ASP107 3.6 75.7 1.0
OD2 B:ASP198 3.8 70.5 1.0
O2B B:DCT605 4.0 65.2 1.0
PA B:DCT605 4.0 85.4 1.0
C5' B:DCT605 4.0 70.5 1.0
OD1 B:ASP198 4.2 72.5 1.0
O3G B:DCT605 4.2 68.4 1.0
OE1 B:GLU199 4.3 67.7 1.0
CG B:ASP198 4.4 63.9 1.0
O5' B:DCT605 4.5 62.3 1.0
C3' P:DC13 4.6 56.8 1.0
CB B:GLU199 4.7 56.0 1.0
O3A B:DCT605 4.8 82.5 1.0
O1A B:DCT605 5.0 83.6 1.0

Reference:

V.Jha, C.Bian, G.Xing, H.Ling. Structure and Mechanism of Error-Free Replication Past the Major Benzo[A]Pyrene Adduct By Human Dna Polymerase Kappa. Nucleic Acids Res. V. 44 4957 2016.
ISSN: ESSN 1362-4962
PubMed: 27034468
DOI: 10.1093/NAR/GKW204
Page generated: Tue Aug 12 00:21:31 2025

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