Magnesium in PDB 6cst: Structure of Human Dna Polymerase Kappa with Dna

Enzymatic activity of Structure of Human Dna Polymerase Kappa with Dna

All present enzymatic activity of Structure of Human Dna Polymerase Kappa with Dna:
2.7.7.7;

Protein crystallography data

The structure of Structure of Human Dna Polymerase Kappa with Dna, PDB code: 6cst was solved by V.Jha, H.Ling, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 44.14 / 2.00
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 67.579, 124.630, 165.040, 90.00, 90.00, 90.00
R / Rfree (%) 19.8 / 23.4

Other elements in 6cst:

The structure of Structure of Human Dna Polymerase Kappa with Dna also contains other interesting chemical elements:

Potassium (K) 4 atoms
Iodine (I) 6 atoms
Chlorine (Cl) 9 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Structure of Human Dna Polymerase Kappa with Dna (pdb code 6cst). 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 with Dna, PDB code: 6cst:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 6cst

Go back to Magnesium Binding Sites List in 6cst
Magnesium binding site 1 out of 4 in the Structure of Human Dna Polymerase Kappa with Dna


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 with Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg601

b:19.5
occ:1.00
 OD1 A:ASP107 2.0 23.4 1.0
O2A A:DZ4619 2.1 22.1 1.0
OD2 A:ASP198 2.1 26.3 1.0
O2G A:DZ4619 2.1 21.9 1.0
O A:MET108 2.1 19.9 1.0
O1B A:DZ4619 2.2 19.6 1.0
CG A:ASP107 3.2 28.3 1.0
CG A:ASP198 3.2 26.1 1.0
PB A:DZ4619 3.2 22.2 1.0
C A:MET108 3.3 21.7 1.0
PA A:DZ4619 3.3 24.7 1.0
PG A:DZ4619 3.4 24.3 1.0
N3A A:DZ4619 3.5 23.3 1.0
O3B A:DZ4619 3.6 23.3 1.0
OD1 A:ASP198 3.6 27.9 1.0
OD2 A:ASP107 3.7 42.0 1.0
MG A:MG602 3.7 42.1 1.0
N A:MET108 3.8 22.6 1.0
NZ A:LYS328 3.9 25.6 1.0
O A:HOH791 3.9 29.3 1.0
O3G A:DZ4619 4.0 22.5 1.0
CA A:MET108 4.0 21.8 1.0
C5' A:DZ4619 4.1 22.9 1.0
C A:ASP107 4.1 22.7 1.0
O5' A:DZ4619 4.2 23.5 1.0
O1A A:DZ4619 4.4 23.5 1.0
N A:ASP109 4.4 20.4 1.0
CB A:ASP107 4.4 25.2 1.0
CB A:ASP198 4.4 26.1 1.0
O A:HOH804 4.4 39.1 1.0
O A:ASP107 4.5 23.5 1.0
CB A:MET108 4.5 22.9 1.0
O1G A:DZ4619 4.5 22.3 1.0
CE A:LYS328 4.6 25.8 1.0
N A:ALA110 4.6 19.6 1.0
O2B A:DZ4619 4.6 23.2 1.0
CA A:ASP107 4.7 23.1 1.0
CA A:ASP109 4.7 22.6 1.0
N A:PHE111 4.7 21.0 1.0
CB A:PHE111 4.8 22.8 1.0
C A:ASP109 4.9 22.9 1.0
O A:ASP198 4.9 25.4 1.0

Magnesium binding site 2 out of 4 in 6cst

Go back to Magnesium Binding Sites List in 6cst
Magnesium binding site 2 out of 4 in the Structure of Human Dna Polymerase Kappa with Dna


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 with Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg602

b:42.1
occ:1.00
 O A:HOH804 2.2 39.1 1.0
OE1 A:GLU199 2.2 38.6 1.0
OD1 A:ASP198 2.4 27.9 1.0
O2A A:DZ4619 2.5 22.1 1.0
OD2 A:ASP107 2.7 42.0 1.0
O3' C:DC13 3.1 44.1 1.0
CD A:GLU199 3.2 41.4 1.0
C3' C:DC13 3.3 37.2 1.0
CG A:ASP107 3.3 28.3 1.0
CG A:ASP198 3.4 26.1 1.0
OD1 A:ASP107 3.5 23.4 1.0
PA A:DZ4619 3.5 24.7 1.0
CG A:GLU199 3.6 36.0 1.0
OD2 A:ASP198 3.6 26.3 1.0
O1A A:DZ4619 3.7 23.5 1.0
CB A:GLU199 3.7 33.2 1.0
MG A:MG601 3.7 19.5 1.0
O5' A:DZ4619 3.9 23.5 1.0
O A:HOH791 4.1 29.3 1.0
C4' C:DC13 4.2 36.2 1.0
C5' A:DZ4619 4.2 22.9 1.0
C5' C:DC13 4.2 35.2 1.0
OG A:SER196 4.4 48.0 1.0
OE2 A:GLU199 4.4 42.2 1.0
C2' C:DC13 4.5 36.3 1.0
NZ A:LYS321 4.5 44.0 1.0
O5' C:DC13 4.5 35.2 1.0
CB A:ASP107 4.6 25.2 1.0
N A:GLU199 4.7 24.9 1.0
CB A:ASP198 4.7 26.1 1.0
C A:ASP198 4.8 25.2 1.0
CA A:GLU199 4.8 29.0 1.0
O A:ASP198 4.8 25.4 1.0
O2G A:DZ4619 4.8 21.9 1.0
N3A A:DZ4619 5.0 23.3 1.0
OP1 C:DC13 5.0 40.4 1.0

Magnesium binding site 3 out of 4 in 6cst

Go back to Magnesium Binding Sites List in 6cst
Magnesium binding site 3 out of 4 in the Structure of Human Dna Polymerase Kappa with Dna


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 with Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg601

b:28.4
occ:1.00
 O2A B:DZ4608 2.0 31.7 1.0
OD1 B:ASP107 2.1 39.4 1.0
O2G B:DZ4608 2.1 30.9 1.0
OD2 B:ASP198 2.2 37.9 1.0
O1B B:DZ4608 2.2 31.1 1.0
O B:MET108 2.3 29.7 1.0
PB B:DZ4608 3.2 31.6 1.0
CG B:ASP107 3.3 36.8 1.0
PA B:DZ4608 3.3 34.2 1.0
CG B:ASP198 3.3 35.4 1.0
PG B:DZ4608 3.4 33.4 1.0
C B:MET108 3.5 27.4 1.0
N3A B:DZ4608 3.5 31.7 1.0
O3B B:DZ4608 3.6 33.2 1.0
NZ B:LYS328 3.7 37.1 1.0
MG B:MG602 3.8 56.0 1.0
OD2 B:ASP107 3.8 42.6 1.0
O B:HOH769 3.9 42.2 1.0
OD1 B:ASP198 3.9 35.4 1.0
N B:MET108 4.0 29.5 1.0
C5' B:DZ4608 4.0 32.8 1.0
O5' B:DZ4608 4.1 34.0 1.0
O3G B:DZ4608 4.1 32.0 1.0
CA B:MET108 4.2 28.9 1.0
C B:ASP107 4.2 33.4 1.0
O1A B:DZ4608 4.4 32.0 1.0
CE B:LYS328 4.4 39.3 1.0
CB B:ASP107 4.5 34.5 1.0
N B:ASP109 4.5 28.5 1.0
CB B:ASP198 4.5 34.5 1.0
O1G B:DZ4608 4.6 30.2 1.0
O2B B:DZ4608 4.6 30.7 1.0
O B:ASP107 4.6 28.8 1.0
N B:ALA110 4.7 27.4 1.0
CA B:ASP107 4.7 32.4 1.0
CA B:ASP109 4.7 30.6 1.0
CB B:MET108 4.7 29.9 1.0
N B:PHE111 4.8 26.8 1.0
CB B:PHE111 4.9 30.2 1.0
C B:ASP109 4.9 32.0 1.0

Magnesium binding site 4 out of 4 in 6cst

Go back to Magnesium Binding Sites List in 6cst
Magnesium binding site 4 out of 4 in the Structure of Human Dna Polymerase Kappa with Dna


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 with Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg602

b:56.0
occ:1.00
 OE2 B:GLU199 2.5 57.9 1.0
OD1 B:ASP198 2.6 35.4 1.0
O2A B:DZ4608 2.7 31.7 1.0
OD2 B:ASP107 3.1 42.6 1.0
CG B:ASP198 3.5 35.4 1.0
CG B:ASP107 3.5 36.8 1.0
OD1 B:ASP107 3.5 39.4 1.0
CD B:GLU199 3.5 57.7 1.0
C3' P:DC13 3.6 44.1 1.0
CB B:GLU199 3.6 41.6 1.0
OD2 B:ASP198 3.6 37.9 1.0
PA B:DZ4608 3.7 34.2 1.0
MG B:MG601 3.8 28.4 1.0
O1A B:DZ4608 3.8 32.0 1.0
O3' P:DC13 3.9 44.7 1.0
CG B:GLU199 3.9 48.2 1.0
C5' P:DC13 4.0 41.2 1.0
O5' B:DZ4608 4.1 34.0 1.0
C4' P:DC13 4.3 41.5 1.0
C5' B:DZ4608 4.4 32.8 1.0
O5' P:DC13 4.4 43.7 1.0
O B:HOH769 4.4 42.2 1.0
OP1 P:DC13 4.5 46.8 1.0
OG B:SER196 4.5 49.7 1.0
OE1 B:GLU199 4.7 51.1 1.0
CB B:ASP107 4.7 34.5 1.0
C2' P:DC13 4.7 40.5 1.0
NZ B:LYS321 4.8 59.5 1.0
CA B:GLU199 4.8 38.2 1.0
CB B:ASP198 4.9 34.5 1.0
C B:ASP198 4.9 34.0 1.0
N B:GLU199 4.9 34.8 1.0
O B:ASP198 4.9 35.0 1.0

Reference:

V.Jha, H.Ling. 2.0 Angstrom Resolution Crystal Structure of Human Pol Kappa Reveals A New Catalytic Function of N-Clasp in Dna Replication. Sci Rep V. 8 15125 2018.
ISSN: ESSN 2045-2322
PubMed: 30310122
DOI: 10.1038/S41598-018-33371-5
Page generated: Mon Dec 14 22:31:59 2020

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