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Magnesium in PDB 5w2c: Structure of Human Dna Polymerase Kappa in Complex with Lucidin- Derived Dna Adduct and Incoming Dampnpp

Enzymatic activity of Structure of Human Dna Polymerase Kappa in Complex with Lucidin- Derived Dna Adduct and Incoming Dampnpp

All present enzymatic activity of Structure of Human Dna Polymerase Kappa in Complex with Lucidin- Derived Dna Adduct and Incoming Dampnpp:
2.7.7.7;

Protein crystallography data

The structure of Structure of Human Dna Polymerase Kappa in Complex with Lucidin- Derived Dna Adduct and Incoming Dampnpp, PDB code: 5w2c 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) 50.01 / 2.50
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 63.709, 128.923, 167.705, 90.00, 90.00, 90.00
R / Rfree (%) 21.1 / 25.3

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Structure of Human Dna Polymerase Kappa in Complex with Lucidin- Derived Dna Adduct and Incoming Dampnpp (pdb code 5w2c). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the Structure of Human Dna Polymerase Kappa in Complex with Lucidin- Derived Dna Adduct and Incoming Dampnpp, PDB code: 5w2c:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in 5w2c

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Magnesium binding site 1 out of 6 in the Structure of Human Dna Polymerase Kappa in Complex with Lucidin- Derived Dna Adduct and Incoming Dampnpp


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 in Complex with Lucidin- Derived Dna Adduct and Incoming Dampnpp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg601

b:46.7
occ:1.00
 O1B A:DZ4608 2.0 53.5 1.0
O1A A:DZ4608 2.1 45.8 1.0
OD1 A:ASP107 2.1 61.0 1.0
O A:MET108 2.1 62.1 1.0
O3G A:DZ4608 2.3 66.2 1.0
OD1 A:ASP198 2.4 60.2 1.0
PB A:DZ4608 3.0 57.3 1.0
CG A:ASP107 3.3 66.6 1.0
PG A:DZ4608 3.3 61.0 1.0
PA A:DZ4608 3.3 63.0 1.0
C A:MET108 3.4 64.3 1.0
O3B A:DZ4608 3.4 59.6 1.0
N3A A:DZ4608 3.5 59.1 1.0
CG A:ASP198 3.5 62.7 1.0
OD2 A:ASP107 3.7 69.8 1.0
O1G A:DZ4608 3.7 68.3 1.0
NZ A:LYS328 3.8 75.5 1.0
OD2 A:ASP198 3.9 70.6 1.0
N A:MET108 4.0 67.1 1.0
MG A:MG603 4.2 72.8 1.0
CA A:MET108 4.2 65.4 1.0
C5' A:DZ4608 4.2 59.2 1.0
O5' A:DZ4608 4.3 60.7 1.0
C A:ASP107 4.3 67.1 1.0
O2B A:DZ4608 4.3 53.5 1.0
N A:ASP109 4.4 58.3 1.0
O2A A:DZ4608 4.4 60.3 1.0
CB A:ASP107 4.5 60.9 1.0
CA A:ASP109 4.6 57.5 1.0
O2G A:DZ4608 4.6 60.6 1.0
N A:ALA110 4.6 51.9 1.0
CB A:MET108 4.6 65.9 1.0
O A:ASP107 4.7 70.6 1.0
CB A:ASP198 4.7 64.5 1.0
CE A:LYS328 4.7 81.3 1.0
CA A:ASP107 4.8 63.3 1.0
C A:ASP109 4.8 54.3 1.0
N A:PHE111 4.9 60.3 1.0
CB A:PHE111 5.0 62.1 1.0

Magnesium binding site 2 out of 6 in 5w2c

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Magnesium binding site 2 out of 6 in the Structure of Human Dna Polymerase Kappa in Complex with Lucidin- Derived Dna Adduct and Incoming Dampnpp


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 in Complex with Lucidin- Derived Dna Adduct and Incoming Dampnpp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg602

b:85.8
occ:1.00
 O A:HOH702 2.3 64.1 1.0
O A:ARG352 2.3 76.9 1.0
OP1 C:DA12 2.3 61.9 1.0
O A:VAL354 2.4 67.7 1.0
O A:ILE357 2.5 70.8 1.0
C A:VAL354 3.4 75.5 1.0
C A:ARG352 3.5 78.3 1.0
C A:ILE357 3.6 61.0 1.0
P C:DA12 3.7 63.3 1.0
N A:ILE357 4.1 66.4 1.0
N A:VAL354 4.1 70.8 1.0
C A:LYS353 4.1 76.4 1.0
N A:SER355 4.1 79.4 1.0
CA A:SER355 4.2 74.5 1.0
NH2 A:ARG352 4.2 82.6 1.0
OP2 C:DA12 4.2 57.6 1.0
CA A:ILE357 4.3 62.8 1.0
N A:GLY356 4.3 69.2 1.0
CA A:VAL354 4.4 73.6 1.0
N A:LYS353 4.4 78.9 1.0
O A:LYS353 4.4 73.5 1.0
CA A:ARG352 4.4 81.5 1.0
CA A:LYS353 4.5 80.5 1.0
CB A:ILE357 4.5 60.4 1.0
CD A:ARG352 4.5 77.2 1.0
N A:GLY358 4.5 57.5 1.0
O5' C:DA12 4.6 67.6 1.0
C A:SER355 4.7 71.8 1.0
O3' C:DG11 4.7 65.9 1.0
CA A:GLY358 4.8 57.6 1.0
CG A:ARG352 4.8 76.1 1.0

Magnesium binding site 3 out of 6 in 5w2c

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Magnesium binding site 3 out of 6 in the Structure of Human Dna Polymerase Kappa in Complex with Lucidin- Derived Dna Adduct and Incoming Dampnpp


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 in Complex with Lucidin- Derived Dna Adduct and Incoming Dampnpp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg603

b:72.8
occ:1.00
 OE1 A:GLU199 2.0 78.8 1.0
O1A A:DZ4608 2.8 45.8 1.0
OD2 A:ASP198 2.9 70.6 1.0
OD2 A:ASP107 3.1 69.8 1.0
CD A:GLU199 3.1 83.4 1.0
C3' C:DC13 3.4 66.1 1.0
CG A:ASP107 3.5 66.6 1.0
CB A:GLU199 3.5 67.7 1.0
OD1 A:ASP107 3.6 61.0 1.0
CG A:GLU199 3.6 78.1 1.0
PA A:DZ4608 3.7 63.0 1.0
O3' C:DC13 3.7 63.1 1.0
O2A A:DZ4608 3.7 60.3 1.0
CG A:ASP198 3.8 62.7 1.0
O A:HOH701 4.0 86.9 1.0
OD1 A:ASP198 4.0 60.2 1.0
O5' C:DC13 4.1 72.1 1.0
C5' C:DC13 4.1 69.7 1.0
MG A:MG601 4.2 46.7 1.0
O5' A:DZ4608 4.2 60.7 1.0
OE2 A:GLU199 4.2 79.4 1.0
C4' C:DC13 4.2 65.5 1.0
OP1 C:DC13 4.2 86.2 1.0
C5' A:DZ4608 4.5 59.2 1.0
CB A:ASP107 4.6 60.9 1.0
C2' C:DC13 4.6 67.1 1.0
NZ A:LYS321 4.7 82.7 1.0
CA A:GLU199 4.8 64.8 1.0
P C:DC13 4.9 79.7 1.0
OG A:SER196 4.9 70.4 1.0
N A:GLU199 4.9 60.3 1.0

Magnesium binding site 4 out of 6 in 5w2c

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Magnesium binding site 4 out of 6 in the Structure of Human Dna Polymerase Kappa in Complex with Lucidin- Derived Dna Adduct and Incoming Dampnpp


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 in Complex with Lucidin- Derived Dna Adduct and Incoming Dampnpp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg601

b:62.7
occ:1.00
 O2B B:DZ4606 1.9 58.6 1.0
O2A B:DZ4606 2.1 62.3 1.0
OD1 B:ASP107 2.1 60.3 1.0
OD1 B:ASP198 2.2 68.1 1.0
O3G B:DZ4606 2.2 66.0 1.0
O B:MET108 2.2 69.7 1.0
PB B:DZ4606 3.1 66.3 1.0
CG B:ASP107 3.3 68.5 1.0
PA B:DZ4606 3.3 62.8 1.0
CG B:ASP198 3.3 75.7 1.0
PG B:DZ4606 3.3 70.1 1.0
C B:MET108 3.4 67.7 1.0
O3B B:DZ4606 3.5 63.2 1.0
N3A B:DZ4606 3.5 63.1 1.0
OD2 B:ASP107 3.8 74.2 1.0
OD2 B:ASP198 3.8 82.2 1.0
MG B:MG603 3.9 95.6 1.0
NZ B:LYS328 3.9 92.9 1.0
N B:MET108 3.9 68.7 1.0
O2G B:DZ4606 4.0 71.9 1.0
C5' B:DZ4606 4.0 60.2 1.0
CA B:MET108 4.1 68.6 1.0
O5' B:DZ4606 4.2 68.9 1.0
C B:ASP107 4.2 66.5 1.0
O1B B:DZ4606 4.3 59.9 1.0
O1A B:DZ4606 4.4 66.1 1.0
N B:ASP109 4.4 70.5 1.0
O1G B:DZ4606 4.5 72.4 1.0
CB B:ASP198 4.5 75.8 1.0
CB B:ASP107 4.6 69.2 1.0
CB B:MET108 4.6 70.9 1.0
O B:ASP107 4.6 70.0 1.0
CA B:ASP109 4.6 72.6 1.0
N B:ALA110 4.6 72.8 1.0
CA B:ASP107 4.8 64.6 1.0
N B:PHE111 4.8 65.2 1.0
CE B:LYS328 4.9 97.1 1.0
C B:ASP109 4.9 70.8 1.0
CB B:PHE111 4.9 67.9 1.0

Magnesium binding site 5 out of 6 in 5w2c

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Magnesium binding site 5 out of 6 in the Structure of Human Dna Polymerase Kappa in Complex with Lucidin- Derived Dna Adduct and Incoming Dampnpp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Structure of Human Dna Polymerase Kappa in Complex with Lucidin- Derived Dna Adduct and Incoming Dampnpp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg602

b:82.5
occ:1.00
 OP1 P:DA12 2.5 67.7 1.0
O B:ILE357 2.6 74.4 1.0
O B:ARG352 2.8 76.2 1.0
O B:VAL354 3.2 71.7 1.0
OP2 P:DA12 3.4 52.4 1.0
P P:DA12 3.4 66.2 1.0
NH2 B:ARG352 3.5 85.3 1.0
O P:HOH111 3.6 71.6 1.0
C B:ILE357 3.7 63.8 1.0
C B:ARG352 4.0 77.5 1.0
C B:VAL354 4.2 70.4 1.0
CD B:ARG352 4.3 77.3 1.0
N B:ILE357 4.5 66.7 1.0
O3' P:DG11 4.5 67.2 1.0
O5' P:DA12 4.5 67.4 1.0
N B:GLY358 4.6 61.0 1.0
CA B:GLY358 4.6 57.4 1.0
CA B:SER355 4.6 71.6 1.0
CZ B:ARG352 4.7 79.9 1.0
CA B:ILE357 4.7 65.0 1.0
N B:GLY356 4.7 69.7 1.0
CG B:ARG352 4.8 80.7 1.0
CA B:ARG352 4.8 75.8 1.0
N B:SER355 4.8 70.8 1.0
C B:LYS353 4.8 79.1 1.0
N B:VAL354 4.9 69.6 1.0
N B:LYS353 4.9 84.7 1.0
NE B:ARG352 5.0 75.9 1.0
CA B:LYS353 5.0 86.2 1.0

Magnesium binding site 6 out of 6 in 5w2c

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Magnesium binding site 6 out of 6 in the Structure of Human Dna Polymerase Kappa in Complex with Lucidin- Derived Dna Adduct and Incoming Dampnpp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Structure of Human Dna Polymerase Kappa in Complex with Lucidin- Derived Dna Adduct and Incoming Dampnpp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg603

b:95.6
occ:1.00
 OE1 B:GLU199 2.3 0.2 1.0
OD2 B:ASP198 2.6 82.2 1.0
O2A B:DZ4606 2.7 62.3 1.0
OD2 B:ASP107 3.1 74.2 1.0
OD1 B:ASP107 3.3 60.3 1.0
CG B:ASP107 3.3 68.5 1.0
CD B:GLU199 3.4 0.2 1.0
C3' P:DC13 3.4 75.9 1.0
O3' P:DC13 3.5 64.2 1.0
CG B:ASP198 3.5 75.7 1.0
CB B:GLU199 3.6 82.0 1.0
PA B:DZ4606 3.7 62.8 1.0
OD1 B:ASP198 3.7 68.1 1.0
CG B:GLU199 3.8 91.0 1.0
O1A B:DZ4606 3.8 66.1 1.0
MG B:MG601 3.9 62.7 1.0
O5' B:DZ4606 4.0 68.9 1.0
C4' P:DC13 4.3 73.7 1.0
C5' B:DZ4606 4.4 60.2 1.0
O5' P:DC13 4.4 84.2 1.0
C5' P:DC13 4.4 78.1 1.0
OE2 B:GLU199 4.4 95.9 1.0
CB B:ASP107 4.5 69.2 1.0
C2' P:DC13 4.6 77.8 1.0
OP1 P:DC13 4.6 91.4 1.0
OG B:SER196 4.8 92.5 1.0
CA B:GLU199 4.8 79.1 1.0
N B:GLU199 4.9 77.2 1.0
O3G B:DZ4606 5.0 66.0 1.0
CB B:ASP198 5.0 75.8 1.0
C B:ASP198 5.0 72.5 1.0

Reference:

O.P.Yockey, V.Jha, P.P.Ghodke, T.Xu, W.Xu, H.Ling, P.I.Pradeepkumar, L.Zhao. Mechanism of Error-Free Dna Replication Past Lucidin-Derived Dna Damage By Human Dna Polymerase Kappa. Chem. Res. Toxicol. V. 30 2023 2017.
ISSN: ISSN 1520-5010
PubMed: 28972744
DOI: 10.1021/ACS.CHEMRESTOX.7B00227
Page generated: Mon Sep 30 06:27:04 2024

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