Atomistry » Sodium » PDB 7kkr-7l00 » 7ksy
Atomistry »
  Sodium »
    PDB 7kkr-7l00 »
      7ksy »

Sodium in PDB 7ksy: Dna Polymerase Mu, Dgtp:Ct Product State Ternary Complex, 10 Mm MG2+ (960MIN)

Enzymatic activity of Dna Polymerase Mu, Dgtp:Ct Product State Ternary Complex, 10 Mm MG2+ (960MIN)

All present enzymatic activity of Dna Polymerase Mu, Dgtp:Ct Product State Ternary Complex, 10 Mm MG2+ (960MIN):
2.7.7.7;

Protein crystallography data

The structure of Dna Polymerase Mu, Dgtp:Ct Product State Ternary Complex, 10 Mm MG2+ (960MIN), PDB code: 7ksy was solved by J.A.Jamsen, S.H.Wilson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 35.04 / 1.58
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 60.316, 62.323, 119.043, 90, 90, 90
R / Rfree (%) 15.6 / 17

Other elements in 7ksy:

The structure of Dna Polymerase Mu, Dgtp:Ct Product State Ternary Complex, 10 Mm MG2+ (960MIN) also contains other interesting chemical elements:

Magnesium (Mg) 1 atom

Sodium Binding Sites:

The binding sites of Sodium atom in the Dna Polymerase Mu, Dgtp:Ct Product State Ternary Complex, 10 Mm MG2+ (960MIN) (pdb code 7ksy). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Dna Polymerase Mu, Dgtp:Ct Product State Ternary Complex, 10 Mm MG2+ (960MIN), PDB code: 7ksy:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 7ksy

Go back to Sodium Binding Sites List in 7ksy
Sodium binding site 1 out of 2 in the Dna Polymerase Mu, Dgtp:Ct Product State Ternary Complex, 10 Mm MG2+ (960MIN)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Dna Polymerase Mu, Dgtp:Ct Product State Ternary Complex, 10 Mm MG2+ (960MIN) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na502

b:21.9
occ:0.99
OD2 A:ASP418 2.1 28.5 1.0
OD1 A:ASP332 2.2 20.3 1.0
OP1 P:DG5 2.3 19.1 1.0
O P:HOH107 2.5 26.9 1.0
OD1 A:ASP330 2.7 22.1 1.0
O3' P:DA4 2.9 18.3 1.0
P P:DG5 3.1 18.1 1.0
CG A:ASP332 3.2 19.7 1.0
CG A:ASP418 3.2 28.8 1.0
CG A:ASP330 3.3 38.5 1.0
MG A:MG501 3.4 20.5 1.0
OD2 A:ASP332 3.5 18.7 1.0
CB A:ASP418 3.9 18.7 1.0
CB A:ASP330 3.9 20.6 1.0
OD2 A:ASP330 4.0 54.2 1.0
C3' P:DA4 4.0 18.0 1.0
C5' P:DA4 4.1 16.6 1.0
OD1 A:ASP418 4.1 23.6 1.0
C4' P:DA4 4.1 16.3 1.0
OP2 P:DG5 4.2 19.8 1.0
O5' P:DG5 4.3 18.8 1.0
NH2 A:ARG416 4.4 20.1 1.0
C5' P:DG5 4.5 17.3 1.0
CB A:ASP332 4.5 17.1 1.0
O2 A:GOA506 4.6 35.8 1.0
O A:VAL331 4.7 19.9 1.0
O P:HOH104 4.7 35.2 1.0
OP1 P:DA4 4.8 18.4 1.0
CZ3 A:TRP434 4.9 21.4 1.0
O5' P:DA4 4.9 17.2 1.0
C A:VAL331 4.9 18.6 1.0
N A:ASP418 4.9 17.7 1.0
CA A:ASP332 5.0 16.4 1.0

Sodium binding site 2 out of 2 in 7ksy

Go back to Sodium Binding Sites List in 7ksy
Sodium binding site 2 out of 2 in the Dna Polymerase Mu, Dgtp:Ct Product State Ternary Complex, 10 Mm MG2+ (960MIN)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Dna Polymerase Mu, Dgtp:Ct Product State Ternary Complex, 10 Mm MG2+ (960MIN) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na503

b:20.8
occ:1.00
O A:VAL246 2.3 18.6 1.0
O P:HOH116 2.4 23.5 1.0
O A:THR241 2.4 22.4 1.0
O A:ILE243 2.4 19.9 1.0
O A:HOH809 2.4 27.9 1.0
OP1 P:DT3 2.7 18.1 1.0
C A:VAL246 3.4 19.3 1.0
C A:THR241 3.4 20.9 1.0
C A:ILE243 3.5 22.0 1.0
O P:HOH110 3.6 38.1 1.0
N A:VAL246 3.7 19.2 1.0
P P:DT3 3.8 18.9 1.0
OP2 P:DT3 4.0 19.8 1.0
O A:HOH698 4.0 41.9 1.0
CA A:VAL246 4.0 18.8 1.0
N A:ILE243 4.1 20.7 1.0
CA A:THR241 4.1 18.9 1.0
C A:GLN242 4.2 23.6 1.0
N A:PHE244 4.3 21.8 1.0
N A:GLY245 4.3 17.8 1.0
CA A:PHE244 4.3 20.0 1.0
CA A:ILE243 4.4 19.9 1.0
N A:GLN242 4.4 23.2 1.0
N A:GLY247 4.4 18.2 1.0
CB A:VAL246 4.5 19.3 1.0
CA A:GLN242 4.5 25.3 1.0
O A:HOH831 4.5 32.9 1.0
O A:HOH817 4.6 48.8 1.0
O A:GLN242 4.6 25.9 1.0
C A:PHE244 4.7 21.7 1.0
O3' P:DG2 4.7 17.9 1.0
CA A:GLY247 4.7 18.1 1.0
CB A:THR241 4.8 20.3 1.0
C A:GLY245 4.8 18.5 1.0
O A:PHE240 4.8 21.4 1.0

Reference:

J.A.Jamsen, A.Sassa, D.D.Shock, W.A.Beard, S.H.Wilson. Dna Polymerase Mu, Dgtp:Ct Product State Ternary Complex, 10 Mm MG2+ (960MIN) To Be Published.
Page generated: Fri Dec 17 11:18:27 2021

Last articles

Zn in 7VD8
Zn in 7V1R
Zn in 7V1Q
Zn in 7VPF
Zn in 7T85
Zn in 7T5F
Zn in 7NF9
Zn in 7M4M
Zn in 7M4O
Zn in 7M4N
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy