Atomistry » Sodium » PDB 3h0n-3hwd » 3h8j
Atomistry »
  Sodium »
    PDB 3h0n-3hwd »
      3h8j »

Sodium in PDB 3h8j: Native T4 Rnase H in the Absence of Divalent Metal Ions

Enzymatic activity of Native T4 Rnase H in the Absence of Divalent Metal Ions

All present enzymatic activity of Native T4 Rnase H in the Absence of Divalent Metal Ions:
3.1.26.4;

Protein crystallography data

The structure of Native T4 Rnase H in the Absence of Divalent Metal Ions, PDB code: 3h8j was solved by S.J.Tomanicek, T.C.Mueser, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.25 / 1.80
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 36.257, 86.458, 57.796, 90.00, 92.04, 90.00
R / Rfree (%) 19.2 / 21.3

Sodium Binding Sites:

The binding sites of Sodium atom in the Native T4 Rnase H in the Absence of Divalent Metal Ions (pdb code 3h8j). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total only one binding site of Sodium was determined in the Native T4 Rnase H in the Absence of Divalent Metal Ions, PDB code: 3h8j:

Sodium binding site 1 out of 1 in 3h8j

Go back to Sodium Binding Sites List in 3h8j
Sodium binding site 1 out of 1 in the Native T4 Rnase H in the Absence of Divalent Metal Ions


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Native T4 Rnase H in the Absence of Divalent Metal Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na306

b:23.1
occ:1.00
OH A:TYR278 2.7 14.8 1.0
O A:MET119 2.9 15.1 1.0
O A:TYR121 2.9 11.7 1.0
O A:LEU115 3.0 10.4 1.0
O A:LYS116 3.3 17.1 1.0
CD A:PRO281 3.3 23.3 1.0
CA A:LYS116 3.5 10.8 1.0
CG A:PRO281 3.5 19.8 1.0
CE1 A:TYR278 3.5 12.2 1.0
CZ A:TYR278 3.6 13.0 1.0
C A:LYS116 3.6 16.8 1.0
C A:LEU115 3.8 12.1 1.0
C A:MET119 4.0 11.8 1.0
C A:TYR121 4.0 14.3 1.0
N A:LYS116 4.1 11.7 1.0
CG2 A:VAL123 4.1 13.9 1.0
N A:TYR121 4.2 13.2 1.0
N A:MET119 4.5 13.0 1.0
O A:HOH577 4.6 23.5 1.0
CB A:LYS116 4.7 14.0 1.0
N A:ALA117 4.7 13.3 1.0
CA A:MET119 4.7 11.5 1.0
CA A:TYR121 4.7 11.9 1.0
N A:PRO281 4.7 21.8 1.0
O A:LYS279 4.8 16.2 1.0
N A:VAL123 4.8 9.1 1.0
CD1 A:LEU280 4.8 18.8 1.0
CD1 A:TYR278 4.9 14.9 1.0
CE2 A:TYR278 4.9 14.3 1.0
CB A:PRO281 4.9 19.5 1.0
CB A:VAL123 4.9 7.9 1.0
O A:HOH424 5.0 26.7 1.0
N A:PRO120 5.0 10.8 1.0

Reference:

S.J.Tomanicek, J.M.Devos, T.C.Mueser. Additional Order Appears in the Absence of Metals in A Fen-1 Protein: Structural Analysis of Magnesium Binding to Bacteriophage T4 Rnaseh To Be Published.
Page generated: Tue Dec 15 06:13:10 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