Atomistry » Magnesium » PDB 1it7-1jbz » 1j2b
Atomistry »
  Magnesium »
    PDB 1it7-1jbz »
      1j2b »

Magnesium 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:

Zinc (Zn) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium 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 Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Crystal Structure of Archaeosine Trna-Guanine Transglycosylase Complexed with Lambda-Form Trna(Val), PDB code: 1j2b:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 1j2b

Go back to Magnesium Binding Sites List in 1j2b
Magnesium binding site 1 out of 4 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 Magnesium with other atoms in the Mg 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
C:Mg1602

b:52.5
occ:1.00
 NH2 A:ARG573 3.7 0.9 1.0
NH1 A:ARG573 3.7 0.0 1.0
C5 C:C972 3.7 0.4 1.0
OP2 C:C972 4.0 97.5 1.0
OP2 C:C973 4.1 93.7 1.0
C5 C:C973 4.1 0.9 1.0
C6 C:C972 4.2 0.4 1.0
CZ A:ARG573 4.2 0.6 1.0
N4 C:C973 4.6 0.6 1.0
C4 C:C972 4.6 0.3 1.0
CE A:LYS576 4.8 0.4 1.0
NZ A:LYS576 4.8 86.8 1.0
O5' C:C972 4.8 0.2 1.0
N4 C:C972 4.9 0.4 1.0
C4 C:C973 4.9 98.1 1.0
N6 C:A974 5.0 0.1 1.0

Magnesium binding site 2 out of 4 in 1j2b

Go back to Magnesium Binding Sites List in 1j2b
Magnesium binding site 2 out of 4 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 Magnesium with other atoms in the Mg 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
A:Mg601

b:85.5
occ:1.00
 O A:MET566 2.5 58.4 1.0
O A:ALA528 2.6 76.0 1.0
O A:PHE569 2.8 80.5 1.0
O A:ILE567 3.2 77.2 1.0
C A:ILE567 3.5 67.9 1.0
C A:ALA528 3.5 73.8 1.0
O A:VAL531 3.7 64.4 1.0
C A:MET566 3.7 61.2 1.0
O A:LYS529 3.8 79.8 1.0
OE1 A:GLN570 3.8 0.1 1.0
N A:PHE569 3.9 60.6 1.0
C A:PHE569 3.9 77.7 1.0
N A:VAL568 4.0 61.1 1.0
CA A:ILE567 4.0 57.4 1.0
CA A:LYS529 4.1 82.4 1.0
C A:LYS529 4.1 76.6 1.0
C A:VAL568 4.1 50.0 1.0
N A:LYS529 4.1 84.1 1.0
N A:VAL531 4.2 62.8 1.0
CA A:VAL568 4.3 55.1 1.0
N A:ILE567 4.3 53.0 1.0
CB A:VAL531 4.3 64.3 1.0
CD A:GLN570 4.4 0.9 1.0
NE2 A:GLN570 4.4 93.9 1.0
CA A:PHE569 4.5 71.2 1.0
CA A:ALA528 4.5 69.3 1.0
C A:VAL531 4.6 49.6 1.0
CA A:VAL531 4.6 55.1 1.0
O A:VAL568 4.8 63.7 1.0
CB A:ALA528 4.8 70.1 1.0
N A:PHE530 4.9 63.7 1.0
CA A:MET566 4.9 57.2 1.0
N A:GLN570 4.9 73.5 1.0

Magnesium binding site 3 out of 4 in 1j2b

Go back to Magnesium Binding Sites List in 1j2b
Magnesium binding site 3 out of 4 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 Magnesium with other atoms in the Mg binding site number 3 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:Mg602

b:38.4
occ:1.00
 NH2 B:ARG573 3.2 0.4 1.0
C5 D:C973 3.7 0.5 1.0
OP2 D:C972 3.8 0.5 1.0
OP2 D:C973 3.9 0.3 1.0
C5 D:C972 4.0 0.7 1.0
CZ B:ARG573 4.1 0.3 1.0
N4 D:C973 4.3 0.8 1.0
C6 D:C972 4.3 0.2 1.0
C4 D:C973 4.4 0.8 1.0
NH1 B:ARG573 4.5 0.2 1.0
O5' D:C972 4.5 0.6 1.0
C6 D:C973 4.6 0.5 1.0
C4 D:C972 4.6 0.8 1.0
P D:C972 4.7 0.1 1.0
N4 D:C972 4.9 0.7 1.0

Magnesium binding site 4 out of 4 in 1j2b

Go back to Magnesium Binding Sites List in 1j2b
Magnesium binding site 4 out of 4 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 Magnesium with other atoms in the Mg binding site number 4 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:Mg1601

b:83.1
occ:1.00
 O B:ALA528 2.9 73.4 1.0
O B:ILE567 3.1 59.0 1.0
O B:MET566 3.1 65.2 1.0
O B:VAL531 3.2 55.2 1.0
O B:PHE569 3.4 77.2 1.0
C B:ILE567 3.5 56.3 1.0
O B:LYS529 3.6 66.3 1.0
NE2 B:GLN570 3.7 79.4 1.0
C B:ALA528 3.9 88.5 1.0
C B:LYS529 4.0 66.3 1.0
CA B:ILE567 4.0 55.6 1.0
N B:VAL531 4.1 67.0 1.0
C B:VAL531 4.2 67.6 1.0
CA B:LYS529 4.2 76.3 1.0
C B:MET566 4.2 65.2 1.0
N B:VAL568 4.2 52.0 1.0
C B:PHE569 4.4 83.5 1.0
N B:LYS529 4.4 87.3 1.0
N B:PHE569 4.4 93.6 1.0
CA B:VAL531 4.5 68.5 1.0
CB B:VAL531 4.5 65.6 1.0
C B:VAL568 4.5 81.1 1.0
CG2 B:VAL531 4.6 62.5 1.0
N B:ILE567 4.6 55.7 1.0
CA B:VAL568 4.6 66.4 1.0
N B:PHE530 4.8 63.0 1.0
CD B:GLN570 4.9 98.8 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: Tue Aug 13 05:44:14 2024

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy