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Magnesium in PDB 5kfp: Human Dna Polymerase Eta-Dna Ternary Complex with Sp-Datp-Alpha-S: Reaction with 20 Mm MG2+ For 600S

Enzymatic activity of Human Dna Polymerase Eta-Dna Ternary Complex with Sp-Datp-Alpha-S: Reaction with 20 Mm MG2+ For 600S

All present enzymatic activity of Human Dna Polymerase Eta-Dna Ternary Complex with Sp-Datp-Alpha-S: Reaction with 20 Mm MG2+ For 600S:
2.7.7.7;

Protein crystallography data

The structure of Human Dna Polymerase Eta-Dna Ternary Complex with Sp-Datp-Alpha-S: Reaction with 20 Mm MG2+ For 600S, PDB code: 5kfp 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) 19.84 / 1.70
Space group P 61
Cell size a, b, c (Å), α, β, γ (°) 98.540, 98.540, 81.590, 90.00, 90.00, 120.00
R / Rfree (%) 17.7 / 22.1

Other elements in 5kfp:

The structure of Human Dna Polymerase Eta-Dna Ternary Complex with Sp-Datp-Alpha-S: Reaction with 20 Mm MG2+ For 600S 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 20 Mm MG2+ For 600S (pdb code 5kfp). 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 20 Mm MG2+ For 600S, PDB code: 5kfp:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in 5kfp

Go back to Magnesium Binding Sites List in 5kfp
Magnesium binding site 1 out of 3 in the Human Dna Polymerase Eta-Dna Ternary Complex with Sp-Datp-Alpha-S: Reaction with 20 Mm MG2+ For 600S


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 20 Mm MG2+ For 600S within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg501

b:26.4
occ:0.45
 OD2 A:ASP13 2.0 26.5 0.6
O A:HOH680 2.2 36.1 1.0
OE2 A:GLU116 2.3 39.7 1.0
OP1 P:AS9 2.4 27.3 0.3
OD1 A:ASP115 2.4 26.2 1.0
O2A A:STP508 2.5 27.4 0.6
O3' P:DT8 2.6 33.4 0.7
O3' P:DT8 2.7 32.7 0.3
MG A:MG504 2.8 26.5 0.5
OD1 A:ASP13 2.8 18.3 0.4
P P:AS9 3.0 32.2 0.3
CG A:ASP13 3.0 22.8 0.6
CD A:GLU116 3.1 35.8 1.0
CG A:ASP13 3.3 22.0 0.4
CG A:ASP115 3.3 24.0 1.0
OD2 A:ASP13 3.4 21.8 0.4
OD1 A:ASP13 3.4 20.2 0.6
C3' P:DT8 3.5 38.5 0.7
OD2 A:ASP115 3.6 23.1 1.0
MG A:MG503 3.6 21.9 0.8
CA A:CA502 3.6 21.9 0.1
PA A:STP508 3.7 30.4 0.6
CB A:GLU116 3.8 29.0 1.0
C3' P:DT8 3.9 36.9 0.3
OE1 A:GLU116 3.9 34.0 1.0
OG A:SER113 3.9 23.4 1.0
CG A:GLU116 3.9 24.2 1.0
C4' P:DT8 4.1 36.8 0.3
O5' A:STP508 4.1 28.8 0.6
C4' P:DT8 4.1 37.3 0.7
O5' P:AS9 4.2 28.8 0.3
C5' P:DT8 4.3 36.5 0.3
CB A:ASP13 4.3 15.6 0.6
NZ A:LYS224 4.3 27.8 0.7
O5 A:DPO509 4.3 20.8 0.3
C5' A:STP508 4.3 28.4 0.6
C5' P:AS9 4.4 28.2 0.3
CB A:ASP13 4.4 15.7 0.4
S2P P:AS9 4.4 41.1 0.3
O1 A:DPO509 4.4 23.3 0.3
C5' P:DT8 4.4 36.7 0.7
O P:HOH105 4.5 43.5 1.0
O1G A:STP508 4.5 20.9 0.6
O A:ASP115 4.5 16.8 1.0
C A:ASP115 4.5 20.4 1.0
S1A A:STP508 4.5 42.8 0.6
N A:GLU116 4.6 14.6 1.0
O A:HOH797 4.7 33.0 1.0
CB A:ASP115 4.7 18.8 1.0
C2' P:DT8 4.8 36.4 0.7
CA A:GLU116 4.8 19.8 1.0
O1B A:STP508 4.9 18.8 0.6
CA A:ASP13 4.9 16.3 0.4
O A:HOH618 4.9 39.0 1.0
CA A:ASP13 5.0 16.2 0.6
C2' P:DT8 5.0 34.5 0.3

Magnesium binding site 2 out of 3 in 5kfp

Go back to Magnesium Binding Sites List in 5kfp
Magnesium binding site 2 out of 3 in the Human Dna Polymerase Eta-Dna Ternary Complex with Sp-Datp-Alpha-S: Reaction with 20 Mm MG2+ For 600S


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 20 Mm MG2+ For 600S within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg503

b:21.9
occ:0.85
 CA A:CA502 0.0 21.9 0.1
O1 A:DPO509 1.6 23.3 0.3
O5 A:DPO509 1.9 20.8 0.3
O1B A:STP508 2.0 18.8 0.6
O1G A:STP508 2.0 20.9 0.6
OD2 A:ASP115 2.2 23.1 1.0
OD1 A:ASP13 2.2 20.2 0.6
OD1 A:ASP13 2.2 18.3 0.4
O A:MET14 2.3 18.2 1.0
O2A A:STP508 2.4 27.4 0.6
OP1 P:AS9 2.4 27.3 0.3
P1 A:DPO509 3.0 24.4 0.3
PB A:STP508 3.1 24.5 0.6
P2 A:DPO509 3.1 24.4 0.3
MG A:MG504 3.1 26.5 0.5
CG A:ASP13 3.2 22.0 0.4
CG A:ASP13 3.2 22.8 0.6
PG A:STP508 3.2 23.8 0.6
CG A:ASP115 3.3 24.0 1.0
C A:MET14 3.4 17.8 1.0
O4 A:DPO509 3.4 24.8 0.3
PA A:STP508 3.5 30.4 0.6
O3B A:STP508 3.6 25.1 0.6
MG A:MG501 3.6 26.4 0.5
OD2 A:ASP13 3.6 21.8 0.4
O3A A:STP508 3.6 30.9 0.6
OD2 A:ASP13 3.6 26.5 0.6
OD1 A:ASP115 3.7 26.2 1.0
O2 A:DPO509 3.8 30.7 0.3
P P:AS9 3.8 32.2 0.3
O7 A:DPO509 3.8 22.1 0.3
O2G A:STP508 3.9 22.4 0.6
C5' A:STP508 3.9 28.4 0.6
N A:MET14 4.0 13.9 1.0
O3 A:DPO509 4.0 23.2 0.3
C5' P:AS9 4.0 28.2 0.3
NZ A:LYS231 4.1 21.2 1.0
O5' P:AS9 4.1 28.8 0.3
N A:CYS16 4.2 16.4 1.0
O5' A:STP508 4.2 28.8 0.6
CA A:MET14 4.2 13.9 1.0
C A:ASP13 4.2 12.8 1.0
O6 A:DPO509 4.3 27.4 0.3
N A:ASP15 4.3 13.8 1.0
O2B A:STP508 4.4 18.2 0.6
O A:HOH797 4.4 33.0 1.0
CA A:ASP15 4.4 15.0 1.0
O3G A:STP508 4.4 27.6 0.6
CB A:ASP13 4.5 15.6 0.6
C A:ASP15 4.5 18.8 1.0
CB A:ASP13 4.5 15.7 0.4
CB A:ASP115 4.5 18.8 1.0
O A:HOH680 4.5 36.1 1.0
N A:PHE17 4.6 13.8 1.0
O A:ASP13 4.6 14.2 1.0
CB A:MET14 4.7 15.3 1.0
CA A:ASP13 4.8 16.3 0.4
CA A:ASP13 4.8 16.2 0.6
O3' P:DT8 4.8 32.7 0.3
CB A:PHE17 4.8 14.3 1.0
O A:ASP115 4.8 16.8 1.0
CA A:CYS16 5.0 15.7 1.0

Magnesium binding site 3 out of 3 in 5kfp

Go back to Magnesium Binding Sites List in 5kfp
Magnesium binding site 3 out of 3 in the Human Dna Polymerase Eta-Dna Ternary Complex with Sp-Datp-Alpha-S: Reaction with 20 Mm MG2+ For 600S


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 20 Mm MG2+ For 600S within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg504

b:26.5
occ:0.45
 O A:HOH797 2.0 33.0 1.0
O A:HOH680 2.0 36.1 1.0
O2A A:STP508 2.0 27.4 0.6
OP1 P:AS9 2.1 27.3 0.3
OD2 A:ASP13 2.4 21.8 0.4
O5 A:DPO509 2.5 20.8 0.3
O1G A:STP508 2.5 20.9 0.6
MG A:MG501 2.8 26.4 0.5
OD2 A:ASP13 2.9 26.5 0.6
OD1 A:ASP13 2.9 20.2 0.6
P P:AS9 3.0 32.2 0.3
PA A:STP508 3.1 30.4 0.6
CA A:CA502 3.1 21.9 0.1
MG A:MG503 3.1 21.9 0.8
CG A:ASP13 3.1 22.0 0.4
OD1 A:ASP13 3.1 18.3 0.4
CG A:ASP13 3.2 22.8 0.6
S1A A:STP508 3.4 42.8 0.6
S2P P:AS9 3.4 41.1 0.3
P2 A:DPO509 3.6 24.4 0.3
O6 A:DPO509 3.7 27.4 0.3
PG A:STP508 3.7 23.8 0.6
O1 A:DPO509 3.8 23.3 0.3
O3A A:STP508 3.8 30.9 0.6
O3G A:STP508 3.8 27.6 0.6
O3' P:DT8 3.8 32.7 0.3
O A:HOH618 4.0 39.0 1.0
O2 A:DPO509 4.0 30.7 0.3
P1 A:DPO509 4.3 24.4 0.3
O4 A:DPO509 4.3 24.8 0.3
NZ A:LYS224 4.3 27.8 0.7
O1B A:STP508 4.3 18.8 0.6
O3' P:DT8 4.4 33.4 0.7
PB A:STP508 4.4 24.5 0.6
O5' P:AS9 4.4 28.8 0.3
O5' A:STP508 4.4 28.8 0.6
O3B A:STP508 4.5 25.1 0.6
C3' P:DT8 4.6 38.5 0.7
CB A:ASP13 4.6 15.6 0.6
OE2 A:GLU116 4.6 39.7 1.0
CB A:ASP13 4.6 15.7 0.4
OD2 A:ASP115 4.6 23.1 1.0
OD1 A:ASP115 4.7 26.2 1.0
O A:HOH606 4.7 42.3 1.0
O A:HOH628 4.7 35.8 1.0
O7 A:DPO509 4.8 22.1 0.3
NZ A:LYS231 4.8 21.2 1.0
C3' P:DT8 4.8 36.9 0.3
O2G A:STP508 4.9 22.4 0.6
CE A:LYS231 5.0 40.8 1.0

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 18:57:26 2024

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