Atomistry » Zinc » PDB 1iml-1jan » 1j2b
Atomistry »
  Zinc »
    PDB 1iml-1jan »
      1j2b »

Zinc in PDB 1j2b: Crystal Structure of Archaeosine Trna-Guanine Transglycosylase Complexed with Lambda-Form Trna(Val)

Enzymatic activity of Crystal Structure of Archaeosine Trna-Guanine Transglycosylase Complexed with Lambda-Form Trna(Val)

All present enzymatic activity of Crystal Structure of Archaeosine Trna-Guanine Transglycosylase Complexed with Lambda-Form Trna(Val):
2.4.2.29;

Protein crystallography data

The structure of Crystal Structure of Archaeosine Trna-Guanine Transglycosylase Complexed with Lambda-Form Trna(Val), PDB code: 1j2b was solved by R.Ishitani, O.Nureki, N.Nameki, N.Okada, S.Nishimura, S.Yokoyama, Riken Structural Genomics/Proteomics Initiative (Rsgi), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.54 / 3.30
Space group H 3 2
Cell size a, b, c (Å), α, β, γ (°) 230.834, 230.834, 269.255, 90.00, 90.00, 120.00
R / Rfree (%) 22.5 / 28.8

Other elements in 1j2b:

The structure of Crystal Structure of Archaeosine Trna-Guanine Transglycosylase Complexed with Lambda-Form Trna(Val) also contains other interesting chemical elements:

Magnesium (Mg) 4 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Archaeosine Trna-Guanine Transglycosylase Complexed with Lambda-Form Trna(Val) (pdb code 1j2b). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Crystal Structure of Archaeosine Trna-Guanine Transglycosylase Complexed with Lambda-Form Trna(Val), PDB code: 1j2b:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 1j2b

Go back to Zinc Binding Sites List in 1j2b
Zinc binding site 1 out of 2 in the Crystal Structure of Archaeosine Trna-Guanine Transglycosylase Complexed with Lambda-Form Trna(Val)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of Archaeosine Trna-Guanine Transglycosylase Complexed with Lambda-Form Trna(Val) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn600

b:76.7
occ:1.00
ND1 A:HIS307 2.1 73.2 1.0
SG A:CYS284 2.5 74.9 1.0
SG A:CYS281 2.7 54.9 1.0
CG A:HIS307 2.9 74.1 1.0
SG A:CYS279 2.9 75.3 1.0
CB A:HIS307 3.1 62.3 1.0
CE1 A:HIS307 3.1 81.8 1.0
OH A:TYR262 3.4 75.2 1.0
CB A:CYS279 3.6 73.8 1.0
CA A:HIS307 3.8 62.8 1.0
CB A:CYS284 3.9 76.7 1.0
CD2 A:HIS307 4.0 72.7 1.0
CB A:CYS281 4.1 72.0 1.0
CZ A:TYR262 4.1 71.5 1.0
NE2 A:HIS307 4.1 76.1 1.0
CE1 A:TYR262 4.1 70.7 1.0
O A:HIS307 4.3 73.0 1.0
C A:HIS307 4.3 69.3 1.0
N A:CYS284 4.4 86.8 1.0
CG2 A:VAL311 4.6 78.2 1.0
CB A:VAL283 4.8 74.8 1.0
CA A:CYS284 4.8 79.5 1.0
N A:CYS281 5.0 97.7 1.0

Zinc binding site 2 out of 2 in 1j2b

Go back to Zinc Binding Sites List in 1j2b
Zinc binding site 2 out of 2 in the Crystal Structure of Archaeosine Trna-Guanine Transglycosylase Complexed with Lambda-Form Trna(Val)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of Archaeosine Trna-Guanine Transglycosylase Complexed with Lambda-Form Trna(Val) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn600

b:70.6
occ:1.00
ND1 B:HIS307 2.1 65.7 1.0
SG B:CYS284 2.3 0.5 1.0
SG B:CYS279 2.3 66.2 1.0
SG B:CYS281 2.5 90.9 1.0
CE1 B:HIS307 2.7 59.2 1.0
CB B:CYS279 3.0 74.1 1.0
CG B:HIS307 3.2 64.8 1.0
CB B:CYS284 3.4 1.0 1.0
CB B:CYS281 3.8 97.6 1.0
CB B:HIS307 3.9 60.9 1.0
NE2 B:HIS307 3.9 66.6 1.0
N B:CYS284 4.0 0.6 1.0
OH B:TYR262 4.1 68.1 1.0
CD2 B:HIS307 4.1 61.5 1.0
CA B:CYS284 4.3 0.6 1.0
CA B:HIS307 4.4 73.3 1.0
N B:CYS281 4.4 97.7 1.0
CE1 B:TYR262 4.5 50.9 1.0
CA B:CYS279 4.5 84.0 1.0
CZ B:TYR262 4.6 57.0 1.0
CA B:CYS281 4.7 92.8 1.0
C B:CYS279 4.9 85.8 1.0
O B:HIS307 4.9 58.5 1.0
N B:SER280 4.9 82.1 1.0
C B:HIS307 5.0 71.0 1.0

Reference:

R.Ishitani, O.Nureki, N.Nameki, N.Okada, S.Nishimura, S.Yokoyama. Alternative Tertiary Structure of Trna For Recognition By A Posttranscriptional Modification Enzyme Cell(Cambridge,Mass.) V. 113 383 2003.
ISSN: ISSN 0092-8674
PubMed: 12732145
DOI: 10.1016/S0092-8674(03)00280-0
Page generated: Wed Dec 16 02:53:14 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