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Magnesium in PDB 5kfn: Human Dna Polymerase Eta-Dna Ternary Complex with Sp-Datp-Alpha-S: Reaction with 1 Mm MG2+ For 1800S

Enzymatic activity of Human Dna Polymerase Eta-Dna Ternary Complex with Sp-Datp-Alpha-S: Reaction with 1 Mm MG2+ For 1800S

All present enzymatic activity of Human Dna Polymerase Eta-Dna Ternary Complex with Sp-Datp-Alpha-S: Reaction with 1 Mm MG2+ For 1800S:
2.7.7.7;

Protein crystallography data

The structure of Human Dna Polymerase Eta-Dna Ternary Complex with Sp-Datp-Alpha-S: Reaction with 1 Mm MG2+ For 1800S, PDB code: 5kfn was solved by Y.Gao, W.Yang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.70 / 1.45
Space group P 61
Cell size a, b, c (Å), α, β, γ (°) 98.470, 98.470, 82.000, 90.00, 90.00, 120.00
R / Rfree (%) 18.8 / 21.7

Other elements in 5kfn:

The structure of Human Dna Polymerase Eta-Dna Ternary Complex with Sp-Datp-Alpha-S: Reaction with 1 Mm MG2+ For 1800S also contains other interesting chemical elements:

Calcium (Ca) 1 atom

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Human Dna Polymerase Eta-Dna Ternary Complex with Sp-Datp-Alpha-S: Reaction with 1 Mm MG2+ For 1800S (pdb code 5kfn). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Human Dna Polymerase Eta-Dna Ternary Complex with Sp-Datp-Alpha-S: Reaction with 1 Mm MG2+ For 1800S, PDB code: 5kfn:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in 5kfn

Go back to Magnesium Binding Sites List in 5kfn
Magnesium binding site 1 out of 3 in the Human Dna Polymerase Eta-Dna Ternary Complex with Sp-Datp-Alpha-S: Reaction with 1 Mm MG2+ For 1800S


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Human Dna Polymerase Eta-Dna Ternary Complex with Sp-Datp-Alpha-S: Reaction with 1 Mm MG2+ For 1800S within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg501

b:16.6
occ:0.45
 OE2 A:GLU116 1.6 19.6 0.5
O A:HOH605 2.0 22.7 0.5
OE1 A:GLU116 2.0 27.1 0.5
OD2 A:ASP13 2.2 19.1 0.2
CD A:GLU116 2.3 23.9 0.5
O2A A:STP507 2.3 18.3 0.9
CG A:GLU116 2.4 13.6 0.5
OD1 A:ASP115 2.6 19.3 1.0
MG A:MG504 2.6 10.8 0.5
O3' P:DT8 2.7 26.4 0.8
CD A:GLU116 3.1 24.2 0.5
C3' P:DT8 3.1 19.1 0.7
OD1 A:ASP13 3.1 13.6 0.8
CG A:ASP13 3.4 14.3 0.2
OD2 A:ASP13 3.4 21.9 0.8
CG A:ASP13 3.5 14.7 0.8
CA A:CA502 3.5 10.8 0.1
MG A:MG503 3.5 10.6 0.8
CG A:ASP115 3.5 14.0 1.0
OE1 A:GLU116 3.5 24.3 0.5
PA A:STP507 3.5 21.4 0.9
OD2 A:ASP115 3.7 16.2 1.0
CB A:GLU116 3.8 20.5 0.5
OE2 A:GLU116 3.9 24.7 0.5
CG A:GLU116 3.9 19.0 0.5
CB A:GLU116 3.9 15.6 0.5
OG A:SER113 3.9 18.5 1.0
C4' P:DT8 3.9 18.7 0.7
O5' A:STP507 4.0 22.0 0.9
C5' P:DT8 4.1 24.0 0.2
S1A A:STP507 4.2 22.4 0.9
OD1 A:ASP13 4.2 15.8 0.2
C5' A:STP507 4.2 24.1 0.9
C5' P:DT8 4.3 24.4 0.8
O A:HOH605 4.3 23.3 0.5
CB A:ASP13 4.4 12.3 0.2
C2' P:DT8 4.4 22.4 0.8
NZ A:LYS224 4.5 24.5 0.7
O1G A:STP507 4.6 16.8 0.9
C A:ASP115 4.6 14.7 1.0
O A:ASP115 4.6 14.8 1.0
CB A:ASP13 4.6 11.9 0.8
N A:GLU116 4.6 13.5 0.5
N A:GLU116 4.7 13.5 0.5
CA A:GLU116 4.7 15.8 0.5
O A:HOH640 4.8 28.7 1.0
CA A:GLU116 4.8 15.9 0.5
CB A:ASP115 4.9 13.6 1.0
O5' P:DT8 4.9 22.1 0.8
O3A A:STP507 4.9 20.9 0.9
O1B A:STP507 4.9 13.3 0.9

Magnesium binding site 2 out of 3 in 5kfn

Go back to Magnesium Binding Sites List in 5kfn
Magnesium binding site 2 out of 3 in the Human Dna Polymerase Eta-Dna Ternary Complex with Sp-Datp-Alpha-S: Reaction with 1 Mm MG2+ For 1800S


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Human Dna Polymerase Eta-Dna Ternary Complex with Sp-Datp-Alpha-S: Reaction with 1 Mm MG2+ For 1800S within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg503

b:10.6
occ:0.80
 CA A:CA502 0.0 10.8 0.1
OD1 A:ASP13 2.0 13.6 0.8
OD2 A:ASP115 2.1 16.2 1.0
O1G A:STP507 2.2 16.8 0.9
O A:MET14 2.2 12.5 1.0
O1B A:STP507 2.2 13.3 0.9
O2A A:STP507 2.3 18.3 0.9
OD1 A:ASP13 2.4 15.8 0.2
OD2 A:ASP13 2.7 19.1 0.2
CG A:ASP13 2.8 14.3 0.2
CG A:ASP13 3.1 14.7 0.8
CG A:ASP115 3.2 14.0 1.0
PB A:STP507 3.3 16.0 0.9
MG A:MG504 3.3 10.8 0.5
C A:MET14 3.4 9.9 1.0
PG A:STP507 3.4 16.5 0.9
PA A:STP507 3.4 21.4 0.9
MG A:MG501 3.5 16.6 0.5
OD1 A:ASP115 3.5 19.3 1.0
OD2 A:ASP13 3.6 21.9 0.8
O3A A:STP507 3.6 20.9 0.9
O3B A:STP507 3.7 18.0 0.9
N A:MET14 3.9 9.9 1.0
C5' A:STP507 3.9 24.1 0.9
O2G A:STP507 4.0 15.0 0.9
NZ A:LYS231 4.0 8.2 0.6
CA A:MET14 4.1 10.6 1.0
C A:ASP13 4.1 10.5 0.2
C A:ASP13 4.1 10.4 0.8
O5' A:STP507 4.2 22.0 0.9
CB A:ASP13 4.2 12.3 0.2
O A:HOH605 4.4 22.7 0.5
CB A:ASP13 4.4 11.9 0.8
N A:ASP15 4.4 8.9 1.0
N A:CYS16 4.5 11.9 1.0
O A:HOH640 4.5 28.7 1.0
CB A:ASP115 4.5 13.6 1.0
O A:ASP13 4.6 11.4 0.2
O A:ASP13 4.6 11.3 0.8
CA A:ASP15 4.6 11.6 1.0
CB A:MET14 4.6 11.2 1.0
CA A:ASP13 4.6 12.3 0.8
CA A:ASP13 4.6 12.3 0.2
O3G A:STP507 4.6 18.7 0.9
O2B A:STP507 4.6 13.6 0.9
C A:ASP15 4.7 11.2 1.0
OE2 A:GLU116 4.7 19.6 0.5
NZ A:LYS231 4.7 19.1 0.4
N A:PHE17 4.7 10.3 1.0
O A:ASP115 4.7 14.8 1.0
CB A:PHE17 4.9 10.8 1.0
S1A A:STP507 5.0 22.4 0.9
CG A:GLU116 5.0 13.6 0.5

Magnesium binding site 3 out of 3 in 5kfn

Go back to Magnesium Binding Sites List in 5kfn
Magnesium binding site 3 out of 3 in the Human Dna Polymerase Eta-Dna Ternary Complex with Sp-Datp-Alpha-S: Reaction with 1 Mm MG2+ For 1800S


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Human Dna Polymerase Eta-Dna Ternary Complex with Sp-Datp-Alpha-S: Reaction with 1 Mm MG2+ For 1800S within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg504

b:10.8
occ:0.45
 O A:HOH605 1.7 22.7 0.5
O2A A:STP507 2.2 18.3 0.9
O A:HOH640 2.2 28.7 1.0
OD2 A:ASP13 2.4 21.9 0.8
OD2 A:ASP13 2.4 19.1 0.2
O A:HOH605 2.5 23.3 0.5
MG A:MG501 2.6 16.6 0.5
OE2 A:GLU116 2.7 19.6 0.5
O1G A:STP507 2.9 16.8 0.9
PA A:STP507 3.1 21.4 0.9
CG A:ASP13 3.1 14.7 0.8
OD1 A:ASP13 3.2 13.6 0.8
S1A A:STP507 3.2 22.4 0.9
CG A:ASP13 3.2 14.3 0.2
CA A:CA502 3.3 10.8 0.1
MG A:MG503 3.3 10.6 0.8
OD1 A:ASP13 3.4 15.8 0.2
OE1 A:GLU116 3.8 27.1 0.5
O A:HOH604 3.8 33.5 1.0
CD A:GLU116 3.9 23.9 0.5
NZ A:LYS231 3.9 19.1 0.4
O3A A:STP507 3.9 20.9 0.9
NZ A:LYS224 4.0 24.5 0.7
PG A:STP507 4.2 16.5 0.9
O3G A:STP507 4.3 18.7 0.9
C3' P:DT8 4.4 19.1 0.7
O5' A:STP507 4.4 22.0 0.9
CB A:ASP13 4.5 12.3 0.2
CG A:GLU116 4.5 13.6 0.5
O3' P:DT8 4.6 26.4 0.8
CB A:ASP13 4.6 11.9 0.8
O1B A:STP507 4.6 13.3 0.9
OD1 A:ASP115 4.7 19.3 1.0
PB A:STP507 4.7 16.0 0.9
CD A:GLU116 4.7 24.2 0.5
OE1 A:GLU116 4.8 24.3 0.5
OD2 A:ASP115 4.8 16.2 1.0
OP1 P:DT8 4.8 20.9 0.8
O3B A:STP507 4.9 18.0 0.9
OE2 A:GLU116 5.0 24.7 0.5

Reference:

Y.Gao, W.Yang. Capture of A Third MG2+ Is Essential For Catalyzing Dna Synthesis. Science V. 352 1334 2016.
ISSN: ESSN 1095-9203
PubMed: 27284197
DOI: 10.1126/SCIENCE.AAD9633
Page generated: Sun Sep 29 18:57:24 2024

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