Atomistry » Manganese » PDB 5jqk-5kg4 » 5kfo
Atomistry »
  Manganese »
    PDB 5jqk-5kg4 »
      5kfo »

Manganese in PDB 5kfo: Human Dna Polymerase Eta-Dna Ternary Complex with Sp-Datp-Alpha-S: Reaction with 1 Mm MN2+ For 1800S

Enzymatic activity of Human Dna Polymerase Eta-Dna Ternary Complex with Sp-Datp-Alpha-S: Reaction with 1 Mm MN2+ For 1800S

All present enzymatic activity of Human Dna Polymerase Eta-Dna Ternary Complex with Sp-Datp-Alpha-S: Reaction with 1 Mm MN2+ 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 MN2+ For 1800S, PDB code: 5kfo 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) 19.94 / 1.52
Space group P 61
Cell size a, b, c (Å), α, β, γ (°) 98.790, 98.790, 82.030, 90.00, 90.00, 120.00
R / Rfree (%) 17.9 / 21.2

Other elements in 5kfo:

The structure of Human Dna Polymerase Eta-Dna Ternary Complex with Sp-Datp-Alpha-S: Reaction with 1 Mm MN2+ For 1800S also contains other interesting chemical elements:

Calcium (Ca) 1 atom

Manganese Binding Sites:

The binding sites of Manganese atom in the Human Dna Polymerase Eta-Dna Ternary Complex with Sp-Datp-Alpha-S: Reaction with 1 Mm MN2+ For 1800S (pdb code 5kfo). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 2 binding sites of Manganese where determined in the Human Dna Polymerase Eta-Dna Ternary Complex with Sp-Datp-Alpha-S: Reaction with 1 Mm MN2+ For 1800S, PDB code: 5kfo:
Jump to Manganese binding site number: 1; 2;

Manganese binding site 1 out of 2 in 5kfo

Go back to Manganese Binding Sites List in 5kfo
Manganese binding site 1 out of 2 in the Human Dna Polymerase Eta-Dna Ternary Complex with Sp-Datp-Alpha-S: Reaction with 1 Mm MN2+ For 1800S


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Human Dna Polymerase Eta-Dna Ternary Complex with Sp-Datp-Alpha-S: Reaction with 1 Mm MN2+ For 1800S within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn501

b:11.4
occ:0.95
OD2 A:ASP13 2.2 12.3 1.0
OE2 A:GLU116 2.2 13.4 1.0
OD1 A:ASP115 2.2 11.8 1.0
O A:HOH747 2.2 15.2 1.0
O2A A:STP506 2.3 13.0 1.0
O3' P:DT8 2.3 12.9 0.9
CG A:ASP115 3.2 11.5 1.0
CD A:GLU116 3.2 14.6 1.0
CG A:ASP13 3.2 10.1 1.0
C3' P:DT8 3.3 13.2 0.9
PA A:STP506 3.5 12.6 1.0
OD2 A:ASP115 3.5 11.3 1.0
OD1 A:ASP13 3.6 12.7 1.0
CA A:CA502 3.6 10.5 0.1
MN A:MN503 3.6 10.3 0.9
OG A:SER113 3.8 12.8 1.0
OE1 A:GLU116 3.8 14.7 1.0
O5' A:STP506 3.9 11.9 1.0
C5' A:STP506 4.1 12.7 1.0
C4' P:DT8 4.1 14.1 1.0
CG A:GLU116 4.1 10.3 1.0
S1A A:STP506 4.2 13.8 1.0
NZ A:LYS224 4.2 12.7 0.8
CB A:GLU116 4.2 11.2 1.0
O A:HOH792 4.2 15.1 1.0
O P:HOH103 4.3 15.7 1.0
CB A:ASP13 4.5 10.1 1.0
C2' P:DT8 4.6 14.0 0.8
CB A:ASP115 4.6 10.3 1.0
C A:ASP115 4.7 10.7 1.0
O A:ASP115 4.7 10.8 1.0
C5' P:DT8 4.8 19.7 0.5
C5' P:DT8 4.8 19.9 0.5
O3A A:STP506 4.8 11.5 1.0
CB A:SER113 4.8 12.0 1.0
O1G A:STP506 4.8 14.6 1.0
N A:GLU116 4.9 9.8 1.0
O5' P:DT8 4.9 23.1 0.5
O A:HOH719 4.9 18.3 1.0

Manganese binding site 2 out of 2 in 5kfo

Go back to Manganese Binding Sites List in 5kfo
Manganese binding site 2 out of 2 in the Human Dna Polymerase Eta-Dna Ternary Complex with Sp-Datp-Alpha-S: Reaction with 1 Mm MN2+ For 1800S


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Human Dna Polymerase Eta-Dna Ternary Complex with Sp-Datp-Alpha-S: Reaction with 1 Mm MN2+ For 1800S within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn503

b:10.3
occ:0.95
CA A:CA502 0.0 10.5 0.1
OD2 A:ASP115 2.1 11.3 1.0
OD1 A:ASP13 2.1 12.7 1.0
O A:MET14 2.2 10.9 1.0
O1G A:STP506 2.2 14.6 1.0
O1B A:STP506 2.3 10.9 1.0
O2A A:STP506 2.4 13.0 1.0
CG A:ASP13 3.1 10.1 1.0
CG A:ASP115 3.2 11.5 1.0
PB A:STP506 3.2 11.5 1.0
C A:MET14 3.3 9.3 1.0
PA A:STP506 3.4 12.6 1.0
OD2 A:ASP13 3.4 12.3 1.0
PG A:STP506 3.4 12.4 1.0
O3A A:STP506 3.5 11.5 1.0
MN A:MN501 3.6 11.4 0.9
OD1 A:ASP115 3.6 11.8 1.0
O3B A:STP506 3.7 12.4 1.0
NZ A:LYS231 3.8 11.9 1.0
N A:MET14 3.8 9.3 1.0
O2G A:STP506 4.0 12.5 1.0
O A:HOH792 4.0 15.1 1.0
C5' A:STP506 4.0 12.7 1.0
CA A:MET14 4.1 9.0 1.0
C A:ASP13 4.2 9.8 1.0
O5' A:STP506 4.2 11.9 1.0
CB A:ASP13 4.3 10.1 1.0
O A:HOH747 4.4 15.2 1.0
N A:ASP15 4.4 9.2 1.0
CB A:ASP115 4.4 10.3 1.0
CE A:LYS231 4.5 17.2 1.0
N A:CYS16 4.5 9.9 1.0
O A:ASP13 4.5 10.2 1.0
O2B A:STP506 4.5 11.4 1.0
CA A:ASP15 4.6 9.3 1.0
CB A:MET14 4.6 11.0 1.0
O3G A:STP506 4.7 14.0 1.0
C A:ASP15 4.7 9.0 1.0
CA A:ASP13 4.7 10.8 1.0
N A:PHE17 4.7 9.6 1.0
O A:ASP115 4.8 10.8 1.0
CB A:PHE17 4.9 9.4 1.0
S1A A:STP506 5.0 13.8 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 Oct 6 01:41:27 2024

Last articles

K in 5FT0
K in 5FIY
K in 5FOG
K in 5FKT
K in 5FKS
K in 5FKQ
K in 5FKR
K in 5FKG
K in 5FKH
K in 5FKF
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy