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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

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