Atomistry » Magnesium » PDB 2hld-2hxf » 2hvq
Atomistry »
  Magnesium »
    PDB 2hld-2hxf »
      2hvq »

Magnesium in PDB 2hvq: Structure of Adenylated Full-Length T4 Rna Ligase 2

Protein crystallography data

The structure of Structure of Adenylated Full-Length T4 Rna Ligase 2, PDB code: 2hvq was solved by J.Nandakumar, C.D.Lima, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 41.56 / 2.40
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 48.020, 57.850, 119.490, 90.00, 90.00, 90.00
R / Rfree (%) 21.1 / 27.4

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Structure of Adenylated Full-Length T4 Rna Ligase 2 (pdb code 2hvq). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Structure of Adenylated Full-Length T4 Rna Ligase 2, PDB code: 2hvq:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 2hvq

Go back to Magnesium Binding Sites List in 2hvq
Magnesium binding site 1 out of 2 in the Structure of Adenylated Full-Length T4 Rna Ligase 2


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of Adenylated Full-Length T4 Rna Ligase 2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg335

b:24.0
occ:1.00
O A:HOH410 2.4 32.2 1.0
OE1 A:GLU204 2.5 25.0 1.0
O A:HOH391 2.6 51.4 1.0
OE2 A:GLU204 2.6 23.1 1.0
O2P A:APK35 2.8 18.4 1.0
CD A:GLU204 2.9 22.7 1.0
ND1 A:HIS37 3.0 22.8 1.0
P A:APK35 3.4 19.8 1.0
NZ A:APK35 3.5 19.3 1.0
O1P A:APK35 3.7 19.3 1.0
CE1 A:HIS37 3.8 25.0 1.0
CG A:HIS37 4.1 22.1 1.0
CA A:HIS37 4.2 10.8 1.0
O A:HOH366 4.2 18.2 1.0
O4' A:APK35 4.3 22.1 1.0
O A:ILE36 4.3 9.0 1.0
CG A:GLU204 4.4 17.8 1.0
CB A:HIS37 4.5 16.5 1.0
CE A:APK35 4.7 9.8 1.0
O5' A:APK35 4.8 23.5 1.0
CG A:APK35 4.9 12.7 1.0
CD A:APK35 4.9 12.6 1.0
OE2 A:GLU99 4.9 16.5 1.0
NE2 A:HIS37 5.0 24.0 1.0

Magnesium binding site 2 out of 2 in 2hvq

Go back to Magnesium Binding Sites List in 2hvq
Magnesium binding site 2 out of 2 in the Structure of Adenylated Full-Length T4 Rna Ligase 2


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of Adenylated Full-Length T4 Rna Ligase 2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg336

b:23.9
occ:1.00
O A:LEU164 2.3 12.0 1.0
OD1 A:ASN166 2.4 23.1 1.0
OH A:TYR206 2.4 11.9 1.0
O A:ILE162 2.5 9.3 1.0
CZ A:TYR206 3.4 12.3 1.0
C A:ILE162 3.4 12.2 1.0
C A:LEU164 3.4 13.0 1.0
CG A:ASN166 3.5 21.4 1.0
CE2 A:TYR206 3.6 5.3 1.0
N A:LEU164 3.6 10.2 1.0
C A:LYS163 3.7 9.3 1.0
ND2 A:ASN166 4.0 19.0 1.0
CA A:LYS163 4.0 10.9 1.0
N A:LYS163 4.0 9.8 1.0
CA A:LEU164 4.1 13.5 1.0
O A:LYS163 4.2 5.5 1.0
N A:ASN166 4.3 15.0 1.0
CA A:ILE162 4.4 11.8 1.0
O A:LEU161 4.5 14.3 1.0
N A:PRO165 4.5 14.5 1.0
C A:PRO165 4.6 15.1 1.0
CE1 A:TYR206 4.6 12.6 1.0
CB A:LEU164 4.7 8.1 1.0
CB A:CYS226 4.7 10.4 1.0
CB A:ASN166 4.7 18.7 1.0
CA A:PRO165 4.7 14.7 1.0
SG A:CYS226 4.7 11.6 1.0
CA A:ASN166 4.8 15.0 1.0
CD2 A:TYR206 4.9 10.3 1.0

Reference:

J.Nandakumar, S.Shuman, C.D.Lima. Rna Ligase Structures Reveal the Basis For Rna Specificity and Conformational Changes That Drive Ligation Forward. Cell(Cambridge,Mass.) V. 127 71 2006.
ISSN: ISSN 0092-8674
PubMed: 17018278
DOI: 10.1016/J.CELL.2006.08.038
Page generated: Mon Dec 14 07:26:30 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy