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Magnesium in PDB 3q1r: Crystal Structure of A Bacterial Rnase P Holoenzyme in Complex with Trna and in the Presence of 5' Leader

Enzymatic activity of Crystal Structure of A Bacterial Rnase P Holoenzyme in Complex with Trna and in the Presence of 5' Leader

All present enzymatic activity of Crystal Structure of A Bacterial Rnase P Holoenzyme in Complex with Trna and in the Presence of 5' Leader:
3.1.26.5;

Protein crystallography data

The structure of Crystal Structure of A Bacterial Rnase P Holoenzyme in Complex with Trna and in the Presence of 5' Leader, PDB code: 3q1r was solved by N.J.Reiter, A.Ostermanm, A.Torres-Larios, K.K.Swinger, T.Pan, A.Mondragon, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.63 / 4.21
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 169.920, 169.920, 185.530, 90.00, 90.00, 120.00
R / Rfree (%) 25.8 / 26.7

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of A Bacterial Rnase P Holoenzyme in Complex with Trna and in the Presence of 5' Leader (pdb code 3q1r). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 5 binding sites of Magnesium where determined in the Crystal Structure of A Bacterial Rnase P Holoenzyme in Complex with Trna and in the Presence of 5' Leader, PDB code: 3q1r:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in 3q1r

Go back to Magnesium Binding Sites List in 3q1r
Magnesium binding site 1 out of 5 in the Crystal Structure of A Bacterial Rnase P Holoenzyme in Complex with Trna and in the Presence of 5' Leader


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 A Bacterial Rnase P Holoenzyme in Complex with Trna and in the Presence of 5' Leader within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg87

b:80.0
occ:1.00
 OP1 C:A83 2.0 80.0 1.0
P C:A83 3.1 80.0 1.0
OP2 C:C84 3.1 80.0 1.0
OP2 C:A83 3.4 80.0 1.0
O5' C:A83 3.8 80.0 1.0
P C:C84 4.2 80.0 1.0
OP1 C:C84 4.2 80.0 1.0
O3' C:C82 4.4 80.0 1.0
C5' C:A83 4.4 80.0 1.0
OP2 B:G224 4.9 80.0 1.0
OP1 B:A223 4.9 80.6 1.0

Magnesium binding site 2 out of 5 in 3q1r

Go back to Magnesium Binding Sites List in 3q1r
Magnesium binding site 2 out of 5 in the Crystal Structure of A Bacterial Rnase P Holoenzyme in Complex with Trna and in the Presence of 5' Leader


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 A Bacterial Rnase P Holoenzyme in Complex with Trna and in the Presence of 5' Leader within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg348

b:80.0
occ:1.00
 OP1 B:G151 3.2 80.0 1.0
OP2 B:A150 3.4 80.0 1.0
OP1 B:G161 4.4 80.0 1.0
P B:G151 4.4 80.0 1.0
C5' B:A150 4.6 80.0 1.0
P B:A150 4.6 80.0 1.0
O3' B:A149 4.7 80.0 1.0
OP2 B:G151 4.8 80.0 1.0
O2' B:A158 4.8 80.0 1.0
OP2 B:C159 5.0 80.0 1.0
O5' B:A150 5.0 80.0 1.0

Magnesium binding site 3 out of 5 in 3q1r

Go back to Magnesium Binding Sites List in 3q1r
Magnesium binding site 3 out of 5 in the Crystal Structure of A Bacterial Rnase P Holoenzyme in Complex with Trna and in the Presence of 5' Leader


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 A Bacterial Rnase P Holoenzyme in Complex with Trna and in the Presence of 5' Leader within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg349

b:80.0
occ:1.00
 OP1 C:G1 2.0 80.0 1.0
O4 B:U52 2.1 80.0 1.0
OP1 B:A50 2.1 80.2 1.0
O3' B:A50 2.4 80.2 1.0
P B:A50 2.6 80.2 1.0
OP2 B:A50 2.7 80.2 1.0
OP3 C:G1 2.9 80.0 1.0
P C:G1 3.0 80.0 1.0
C3' B:A50 3.0 80.8 1.0
C5' B:A50 3.2 80.8 1.0
C4 B:U52 3.2 80.0 1.0
O5' B:A50 3.4 80.2 1.0
O5' C:G1 3.5 80.0 1.0
OP2 B:G51 3.5 80.0 1.0
C4' B:A50 3.5 80.8 1.0
P B:G51 3.6 80.0 1.0
C5 B:U52 3.9 80.0 1.0
O3' B:A49 4.1 80.9 1.0
OP2 C:G2 4.2 80.0 1.0
N3 B:U52 4.3 80.0 1.0
OP2 C:G1 4.4 80.0 1.0
OP1 B:G51 4.4 80.0 1.0
C2' B:A50 4.5 80.8 1.0
OP1 C:G2 4.6 80.0 1.0
O3' C:G1 4.6 80.0 1.0
P C:G2 4.7 80.0 1.0
O5' B:G51 4.7 80.0 1.0
O4' B:A50 4.8 80.8 1.0
MG B:MG350 4.8 80.0 1.0
OP1 B:A323 4.8 80.6 1.0
C5' C:G1 4.9 80.0 1.0
OP2 B:A323 5.0 80.6 1.0

Magnesium binding site 4 out of 5 in 3q1r

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Magnesium binding site 4 out of 5 in the Crystal Structure of A Bacterial Rnase P Holoenzyme in Complex with Trna and in the Presence of 5' Leader


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 A Bacterial Rnase P Holoenzyme in Complex with Trna and in the Presence of 5' Leader within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg350

b:80.0
occ:1.00
 OP2 B:G51 2.2 80.0 1.0
OP1 B:G51 3.0 80.0 1.0
P B:G51 3.0 80.0 1.0
O3' D:U-1 3.4 80.2 1.0
CE A:LYS56 3.9 80.0 1.0
OP3 C:G1 3.9 80.0 1.0
OP1 C:G1 4.1 80.0 1.0
O5' B:G51 4.2 80.0 1.0
O3' B:A50 4.2 80.2 1.0
NZ A:LYS56 4.3 80.0 1.0
P C:G1 4.3 80.0 1.0
OP2 C:G1 4.4 80.0 1.0
CD A:LYS56 4.4 80.0 1.0
NH2 A:ARG52 4.5 80.0 1.0
C3' D:U-1 4.5 80.2 1.0
C5' B:G51 4.7 80.0 1.0
C4' B:A50 4.8 80.8 1.0
MG B:MG349 4.8 80.0 1.0

Magnesium binding site 5 out of 5 in 3q1r

Go back to Magnesium Binding Sites List in 3q1r
Magnesium binding site 5 out of 5 in the Crystal Structure of A Bacterial Rnase P Holoenzyme in Complex with Trna and in the Presence of 5' Leader


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Crystal Structure of A Bacterial Rnase P Holoenzyme in Complex with Trna and in the Presence of 5' Leader within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg351

b:80.5
occ:1.00
 C5' B:G1 3.4 80.0 1.0
OP1 B:G1 4.0 80.0 1.0
C4' B:G1 4.1 80.0 1.0
O5' B:G1 4.3 80.0 1.0
O4' B:G1 4.4 80.0 1.0
P B:G1 4.7 80.0 1.0

Reference:

N.J.Reiter, A.Osterman, A.Torres-Larios, K.K.Swinger, T.Pan, A.Mondragon. Structure of A Bacterial Ribonuclease P Holoenzyme in Complex with Trna. Nature V. 468 784 2010.
ISSN: ISSN 0028-0836
PubMed: 21076397
DOI: 10.1038/NATURE09516
Page generated: Mon Aug 11 02:16:21 2025

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