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Magnesium in PDB 3in5: Structure of Human Dna Polymerase Kappa Inserting Datp Opposite An 8-Oxog Dna Lesion

Enzymatic activity of Structure of Human Dna Polymerase Kappa Inserting Datp Opposite An 8-Oxog Dna Lesion

All present enzymatic activity of Structure of Human Dna Polymerase Kappa Inserting Datp Opposite An 8-Oxog Dna Lesion:
2.7.7.7;

Protein crystallography data

The structure of Structure of Human Dna Polymerase Kappa Inserting Datp Opposite An 8-Oxog Dna Lesion, PDB code: 3in5 was solved by T.D.Silverstein, R.Vasquez-Del Carpio, A.K.Aggarwal, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.12 / 3.20
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 116.846, 154.480, 217.293, 90.00, 90.00, 90.00
R / Rfree (%) 22.5 / 27.4

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Structure of Human Dna Polymerase Kappa Inserting Datp Opposite An 8-Oxog Dna Lesion (pdb code 3in5). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Structure of Human Dna Polymerase Kappa Inserting Datp Opposite An 8-Oxog Dna Lesion, PDB code: 3in5:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 3in5

Go back to Magnesium Binding Sites List in 3in5
Magnesium binding site 1 out of 4 in the Structure of Human Dna Polymerase Kappa Inserting Datp Opposite An 8-Oxog Dna Lesion


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of Human Dna Polymerase Kappa Inserting Datp Opposite An 8-Oxog Dna Lesion within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg2

b:26.2
occ:1.00
OD2 A:ASP198 1.9 40.5 1.0
OD1 A:ASP107 2.1 38.7 1.0
O1A A:ATP1 2.1 35.2 1.0
O1B A:ATP1 2.3 33.5 1.0
O A:MET108 2.3 35.6 1.0
O1G A:ATP1 2.5 34.8 1.0
CG A:ASP198 3.1 42.1 1.0
CG A:ASP107 3.3 36.7 1.0
PA A:ATP1 3.5 34.0 1.0
C A:MET108 3.5 35.0 1.0
PB A:ATP1 3.5 33.3 1.0
NZ A:LYS328 3.7 45.0 1.0
N A:MET108 3.7 35.1 1.0
OD1 A:ASP198 3.8 44.2 1.0
O3A A:ATP1 3.8 33.6 1.0
O A:HOH527 3.8 35.8 1.0
PG A:ATP1 3.9 35.4 1.0
C A:ASP107 4.0 35.1 1.0
OD2 A:ASP107 4.0 38.0 1.0
C5' A:ATP1 4.1 31.6 1.0
CA A:MET108 4.1 35.0 1.0
O3B A:ATP1 4.2 33.5 1.0
CB A:ASP198 4.2 41.2 1.0
O5' A:ATP1 4.3 31.6 1.0
CB A:ASP107 4.4 35.7 1.0
O A:ASP107 4.4 35.1 1.0
CA A:ASP107 4.5 35.4 1.0
CE A:LYS328 4.5 44.6 1.0
N A:ASP109 4.6 34.4 1.0
OE1 A:GLU199 4.6 49.1 1.0
CB A:MET108 4.6 35.0 1.0
O2A A:ATP1 4.6 34.6 1.0
O A:ASP198 4.7 40.1 1.0
O3G A:ATP1 4.7 35.3 1.0
O2B A:ATP1 4.8 34.9 1.0
CA A:ASP109 4.8 34.3 1.0
CB A:PHE111 4.8 34.0 1.0
CG A:GLU199 4.9 44.2 1.0
N A:ALA110 5.0 34.0 1.0

Magnesium binding site 2 out of 4 in 3in5

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Magnesium binding site 2 out of 4 in the Structure of Human Dna Polymerase Kappa Inserting Datp Opposite An 8-Oxog Dna Lesion


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of Human Dna Polymerase Kappa Inserting Datp Opposite An 8-Oxog Dna Lesion within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg3

b:41.0
occ:1.00
O A:ILE357 2.4 38.7 1.0
O A:VAL354 2.6 37.3 1.0
O A:ARG352 2.6 34.7 1.0
OP1 P:DT12 2.7 41.4 1.0
C A:ILE357 3.5 38.5 1.0
C A:VAL354 3.6 37.1 1.0
C A:ARG352 3.7 35.1 1.0
NE A:ARG352 3.9 35.6 1.0
P P:DT12 3.9 40.9 1.0
CD A:ARG352 3.9 36.5 1.0
N A:ILE357 4.0 37.9 1.0
N A:VAL354 4.1 36.9 1.0
N A:GLY356 4.2 37.1 1.0
CA A:ILE357 4.2 38.1 1.0
OP2 P:DT12 4.3 39.8 1.0
CB A:ILE357 4.3 38.1 1.0
CA A:SER355 4.4 37.1 1.0
C A:LYS353 4.4 36.8 1.0
N A:SER355 4.4 37.2 1.0
CA A:ARG352 4.4 34.8 1.0
CA A:VAL354 4.5 37.0 1.0
N A:GLY358 4.6 39.1 1.0
CG A:ARG352 4.6 35.8 1.0
N A:LYS353 4.6 35.7 1.0
CA A:LYS353 4.7 36.5 1.0
C A:SER355 4.7 36.8 1.0
CA A:GLY358 4.8 39.5 1.0
O3' P:DC11 4.8 41.2 1.0
O A:LYS353 4.8 37.3 1.0
C A:GLY356 4.9 37.8 1.0
O5' P:DT12 5.0 40.8 1.0

Magnesium binding site 3 out of 4 in 3in5

Go back to Magnesium Binding Sites List in 3in5
Magnesium binding site 3 out of 4 in the Structure of Human Dna Polymerase Kappa Inserting Datp Opposite An 8-Oxog Dna Lesion


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Structure of Human Dna Polymerase Kappa Inserting Datp Opposite An 8-Oxog Dna Lesion within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1

b:37.6
occ:1.00
O2B B:ATP2 1.8 55.6 1.0
O1A B:ATP2 2.0 54.3 1.0
O1G B:ATP2 2.2 57.9 1.0
OD1 B:ASP107 2.2 55.4 1.0
O B:MET108 2.5 55.5 1.0
OD2 B:ASP198 2.7 67.3 1.0
PB B:ATP2 2.8 54.6 1.0
PA B:ATP2 3.0 53.6 1.0
O3A B:ATP2 3.1 53.5 1.0
CG B:ASP107 3.3 54.6 1.0
PG B:ATP2 3.4 59.8 1.0
O3B B:ATP2 3.4 57.3 1.0
OD2 B:ASP107 3.6 55.6 1.0
C B:MET108 3.6 55.4 1.0
O5' B:ATP2 3.8 52.8 1.0
CG B:ASP198 3.9 66.8 1.0
C5' B:ATP2 3.9 52.0 1.0
NZ B:LYS328 4.1 60.4 1.0
O2G B:ATP2 4.1 59.2 1.0
OE1 B:GLU199 4.2 65.8 1.0
N B:MET108 4.2 54.5 1.0
O1B B:ATP2 4.2 54.1 1.0
CE B:LYS328 4.2 61.3 1.0
O2A B:ATP2 4.3 55.8 1.0
N B:ALA110 4.4 56.7 1.0
CA B:MET108 4.4 55.2 1.0
O3G B:ATP2 4.6 59.2 1.0
OD1 B:ASP198 4.6 67.9 1.0
N B:PHE111 4.6 58.0 1.0
C B:ASP107 4.6 53.6 1.0
CB B:ASP107 4.6 53.6 1.0
N B:ASP109 4.6 55.7 1.0
CB B:PHE111 4.7 58.5 1.0
CA B:ASP109 4.8 56.0 1.0
CB B:ASP198 4.8 66.1 1.0
C B:ASP109 4.9 56.3 1.0
CB B:MET108 5.0 55.5 1.0
CD B:GLU199 5.0 66.2 1.0

Magnesium binding site 4 out of 4 in 3in5

Go back to Magnesium Binding Sites List in 3in5
Magnesium binding site 4 out of 4 in the Structure of Human Dna Polymerase Kappa Inserting Datp Opposite An 8-Oxog Dna Lesion


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Structure of Human Dna Polymerase Kappa Inserting Datp Opposite An 8-Oxog Dna Lesion within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg4

b:57.5
occ:1.00
OP1 Q:DT12 2.5 45.4 1.0
O B:VAL354 2.6 43.3 1.0
O B:ARG352 2.7 43.3 1.0
O B:ILE357 2.7 40.2 1.0
C B:VAL354 3.6 43.1 1.0
C B:ILE357 3.6 40.2 1.0
P Q:DT12 3.7 44.5 1.0
N B:ILE357 3.7 40.6 1.0
N B:GLY356 3.8 42.0 1.0
C B:ARG352 3.8 42.9 1.0
CA B:SER355 4.0 43.4 1.0
OP2 Q:DT12 4.1 42.3 1.0
NH1 B:ARG352 4.1 49.8 1.0
CA B:ILE357 4.2 40.1 1.0
N B:SER355 4.2 43.4 1.0
C B:SER355 4.4 42.5 1.0
C B:LYS353 4.4 42.7 1.0
N B:VAL354 4.4 42.5 1.0
CB B:ILE357 4.4 40.1 1.0
O5' Q:DT12 4.5 47.6 1.0
O B:LYS353 4.6 42.3 1.0
CA B:VAL354 4.6 42.6 1.0
C B:GLY356 4.6 41.2 1.0
N B:GLY358 4.6 40.0 1.0
CA B:ARG352 4.7 42.7 1.0
NZ B:LYS25 4.7 92.2 1.0
CA B:GLY356 4.8 41.6 1.0
N B:LYS353 4.8 43.0 1.0
CA B:LYS353 4.8 43.0 1.0
O3' Q:DC11 4.9 45.1 1.0
CG B:ARG352 4.9 45.1 1.0
CA B:GLY358 5.0 40.0 1.0
CE B:LYS25 5.0 92.3 1.0

Reference:

R.Vasquez-Del Carpio, T.D.Silverstein, S.Lone, M.K.Swan, J.R.Choudhury, R.E.Johnson, S.Prakash, L.Prakash, A.K.Aggarwal. Structure of Human Dna Polymerase Kappa Inserting Datp Opposite An 8-Oxog Dna Lesion Plos One V. 4 E5766 2009.
ISSN: ESSN 1932-6203
PubMed: 19492058
DOI: 10.1371/JOURNAL.PONE.0005766
Page generated: Mon Dec 14 08:17:20 2020

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