Atomistry » Magnesium » PDB 3py8-3q86 » 3q1r
Atomistry »
  Magnesium »
    PDB 3py8-3q86 »
      3q1r »

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

Go back to Magnesium Binding Sites List in 3q1r
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: Thu Aug 15 09:52:14 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