Magnesium in PDB 6dt1: Crystal Structure of the Ligase From Bacteriophage T4 Complexed with Dna Intermediate

Enzymatic activity of Crystal Structure of the Ligase From Bacteriophage T4 Complexed with Dna Intermediate

All present enzymatic activity of Crystal Structure of the Ligase From Bacteriophage T4 Complexed with Dna Intermediate:
6.5.1.1;

Protein crystallography data

The structure of Crystal Structure of the Ligase From Bacteriophage T4 Complexed with Dna Intermediate, PDB code: 6dt1 was solved by K.Shi, H.Aihara, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 113.02 / 2.75
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 63.526, 67.429, 114.635, 88.78, 80.94, 62.97
R / Rfree (%) 17 / 21.9

Other elements in 6dt1:

The structure of Crystal Structure of the Ligase From Bacteriophage T4 Complexed with Dna Intermediate also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of the Ligase From Bacteriophage T4 Complexed with Dna Intermediate (pdb code 6dt1). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total only one binding site of Magnesium was determined in the Crystal Structure of the Ligase From Bacteriophage T4 Complexed with Dna Intermediate, PDB code: 6dt1:

Magnesium binding site 1 out of 1 in 6dt1

Go back to Magnesium Binding Sites List in 6dt1
Magnesium binding site 1 out of 1 in the Crystal Structure of the Ligase From Bacteriophage T4 Complexed with Dna Intermediate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of the Ligase From Bacteriophage T4 Complexed with Dna Intermediate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg517

b:51.6
occ:1.00
 OE2 A:GLU217 2.5 32.5 1.0
O C:HOH204 2.6 38.2 1.0
O A:HOH639 2.9 34.0 1.0
O A:HOH616 3.0 61.5 1.0
O2' C:AMP100 3.1 34.4 1.0
OE1 A:GLU217 3.3 38.8 1.0
CD A:GLU217 3.3 36.7 1.0
C1' C:AMP100 3.5 35.2 1.0
OP2 C:DG12 3.6 43.1 1.0
C5' B:DOC11 3.6 33.0 1.0
C2' C:AMP100 3.8 36.1 1.0
OP1 C:DG12 3.9 40.4 1.0
O A:GLY162 3.9 47.1 1.0
O4' C:AMP100 4.0 36.3 1.0
OP1 B:DOC11 4.0 28.6 1.0
C4' C:AMP100 4.1 38.1 1.0
O A:ALA160 4.1 31.0 1.0
N A:ARG164 4.2 30.1 1.0
P C:DG12 4.2 43.5 1.0
C3' C:AMP100 4.4 40.3 1.0
O5' B:DOC11 4.4 30.7 1.0
O3' C:AMP100 4.4 33.6 1.0
C A:GLY162 4.4 35.9 1.0
C4' B:DOC11 4.4 34.3 1.0
N A:GLY162 4.6 38.1 1.0
C3' B:DOC11 4.6 29.0 1.0
N9 C:AMP100 4.6 39.3 1.0
O A:HOH682 4.7 60.3 1.0
CA A:ALA163 4.7 34.6 1.0
CG A:GLU217 4.8 30.0 1.0
C A:ALA163 4.8 37.1 1.0
CB A:ARG164 4.8 30.3 1.0
N A:ALA163 4.9 29.1 1.0
CA A:ARG164 4.9 29.2 1.0
P B:DOC11 4.9 35.1 1.0
C8 C:AMP100 4.9 36.9 1.0
NZ A:LYS159 5.0 41.2 1.0

Reference:

K.Shi, T.E.Bohl, J.Park, A.Zasada, S.Malik, S.Banerjee, V.Tran, N.Li, Z.Yin, F.Kurniawan, K.Orellana, H.Aihara. T4 Dna Ligase Structure Reveals A Prototypical Atp-Dependent Ligase with A Unique Mode of Sliding Clamp Interaction. Nucleic Acids Res. V. 46 10474 2018.
ISSN: ESSN 1362-4962
PubMed: 30169742
DOI: 10.1093/NAR/GKY776
Page generated: Mon Dec 14 22:36:54 2020

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