Atomistry » Calcium » PDB 4fsd-4gg1 » 4g26
Atomistry »
  Calcium »
    PDB 4fsd-4gg1 »
      4g26 »

Calcium in PDB 4g26: Crystal Structure of Proteinaceous Rnase P 1 (PRORP1) From A. Thaliana with Ca

Enzymatic activity of Crystal Structure of Proteinaceous Rnase P 1 (PRORP1) From A. Thaliana with Ca

All present enzymatic activity of Crystal Structure of Proteinaceous Rnase P 1 (PRORP1) From A. Thaliana with Ca:
3.1.26.5;

Protein crystallography data

The structure of Crystal Structure of Proteinaceous Rnase P 1 (PRORP1) From A. Thaliana with Ca, PDB code: 4g26 was solved by M.Koutmos, M.J.Howard, C.A.Fierke, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 43.09 / 1.75
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 41.790, 111.883, 140.073, 90.00, 90.00, 90.00
R / Rfree (%) 16.2 / 20.9

Other elements in 4g26:

The structure of Crystal Structure of Proteinaceous Rnase P 1 (PRORP1) From A. Thaliana with Ca also contains other interesting chemical elements:

Zinc (Zn) 1 atom

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Proteinaceous Rnase P 1 (PRORP1) From A. Thaliana with Ca (pdb code 4g26). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 5 binding sites of Calcium where determined in the Crystal Structure of Proteinaceous Rnase P 1 (PRORP1) From A. Thaliana with Ca, PDB code: 4g26:
Jump to Calcium binding site number: 1; 2; 3; 4; 5;

Calcium binding site 1 out of 5 in 4g26

Go back to Calcium Binding Sites List in 4g26
Calcium binding site 1 out of 5 in the Crystal Structure of Proteinaceous Rnase P 1 (PRORP1) From A. Thaliana with Ca


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of Proteinaceous Rnase P 1 (PRORP1) From A. Thaliana with Ca within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1002

b:48.2
occ:0.80
 OD1 A:ASP475 2.3 28.5 1.0
O A:HOH1237 2.5 34.0 1.0
O A:HOH1116 2.5 25.8 1.0
O A:HOH1301 2.5 49.1 1.0
O A:HOH1324 2.9 45.3 1.0
O A:HOH1169 2.9 32.9 1.0
CG A:ASP475 3.4 29.9 1.0
OD2 A:ASP475 3.7 34.3 1.0
OD1 A:ASP474 3.7 48.3 0.0
OD2 A:ASP493 3.9 34.0 1.0
O A:HOH1108 4.0 34.0 1.0
CZ2 A:TRP478 4.4 26.4 1.0
NE1 A:TRP478 4.4 23.9 1.0
OD2 A:ASP399 4.5 24.6 1.0
OD1 A:ASP399 4.6 23.3 1.0
CB A:ASP475 4.7 33.4 1.0
CG A:ASP474 4.7 43.7 0.0
CE2 A:TRP478 4.8 26.7 1.0
N A:ASP475 4.8 24.3 1.0
OD1 A:ASN473 4.9 31.1 1.0
CG A:ASP399 5.0 23.5 1.0

Calcium binding site 2 out of 5 in 4g26

Go back to Calcium Binding Sites List in 4g26
Calcium binding site 2 out of 5 in the Crystal Structure of Proteinaceous Rnase P 1 (PRORP1) From A. Thaliana with Ca


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of Proteinaceous Rnase P 1 (PRORP1) From A. Thaliana with Ca within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1003

b:75.6
occ:1.00
 O A:HOH1107 2.2 40.8 1.0
O A:HOH1243 2.5 31.7 1.0
O A:HOH1126 2.6 20.1 1.0
O A:HOH1151 3.1 25.3 1.0
O A:PRO393 3.7 19.3 1.0
C A:GLY392 3.8 19.2 1.0
O A:GLY392 3.8 22.8 1.0
O A:HOH1118 3.9 22.3 1.0
CE1 A:PHE394 4.0 20.2 1.0
CA A:GLY392 4.0 18.6 1.0
O A:ALA462 4.1 19.4 1.0
O A:GLY463 4.3 18.7 1.0
N A:GLY392 4.3 16.9 1.0
N A:PRO393 4.4 19.1 1.0
CD1 A:PHE394 4.4 20.5 1.0
CZ A:PHE394 4.6 18.5 1.0
C A:PRO393 4.7 19.1 1.0
O A:HOH1121 4.8 23.2 1.0
C A:GLY463 4.8 17.7 1.0
CD A:PRO393 4.8 18.1 1.0

Calcium binding site 3 out of 5 in 4g26

Go back to Calcium Binding Sites List in 4g26
Calcium binding site 3 out of 5 in the Crystal Structure of Proteinaceous Rnase P 1 (PRORP1) From A. Thaliana with Ca


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of Proteinaceous Rnase P 1 (PRORP1) From A. Thaliana with Ca within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1004

b:30.0
occ:1.00
 NZ A:LYS451 3.4 27.6 1.0
O A:HOH1326 3.4 35.4 1.0
CD A:LYS451 3.9 27.2 1.0
CE A:LYS451 4.0 27.5 1.0
CG A:LYS451 5.0 24.2 1.0

Calcium binding site 4 out of 5 in 4g26

Go back to Calcium Binding Sites List in 4g26
Calcium binding site 4 out of 5 in the Crystal Structure of Proteinaceous Rnase P 1 (PRORP1) From A. Thaliana with Ca


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystal Structure of Proteinaceous Rnase P 1 (PRORP1) From A. Thaliana with Ca within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1005

b:65.5
occ:1.00
 O A:HOH1101 2.1 34.5 1.0
O A:HOH1479 2.1 32.8 1.0
N A:PHE413 3.0 23.0 1.0
O A:HOH1366 3.2 54.0 1.0
O A:HOH1339 3.5 51.3 1.0
O A:PHE411 3.6 28.5 1.0
CB A:PHE413 3.7 24.6 1.0
CA A:SER412 3.8 28.4 1.0
CA A:PHE413 3.8 21.3 1.0
C A:SER412 3.8 23.9 1.0
N A:PHE414 4.2 19.3 1.0
C A:PHE411 4.5 27.9 1.0
C A:PHE413 4.6 18.1 1.0
N A:SER412 4.6 24.3 1.0
OG A:SER412 4.7 22.2 1.0
CB A:SER412 4.8 27.1 1.0
O A:HOH1138 4.9 34.8 1.0
O A:HOH1422 4.9 42.9 1.0

Calcium binding site 5 out of 5 in 4g26

Go back to Calcium Binding Sites List in 4g26
Calcium binding site 5 out of 5 in the Crystal Structure of Proteinaceous Rnase P 1 (PRORP1) From A. Thaliana with Ca


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Crystal Structure of Proteinaceous Rnase P 1 (PRORP1) From A. Thaliana with Ca within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1006

b:29.2
occ:1.00
 O A:HOH1123 3.1 26.6 1.0
NH1 A:ARG431 3.2 23.3 1.0
NH2 A:ARG431 3.4 23.5 1.0
CZ A:ARG431 3.8 20.8 1.0
O A:HOH1219 4.5 37.1 1.0
O A:HOH1111 4.6 23.5 1.0
O A:HOH1157 4.8 34.3 1.0
OD1 A:ASP395 4.9 24.2 1.0

Reference:

M.J.Howard, W.H.Lim, C.A.Fierke, M.Koutmos. Mitochondrial Ribonuclease P Structure Provides Insight Into the Evolution of Catalytic Strategies For Precursor-Trna 5' Processing. Proc.Natl.Acad.Sci.Usa V. 109 16149 2012.
ISSN: ISSN 0027-8424
PubMed: 22991464
DOI: 10.1073/PNAS.1209062109
Page generated: Sat Dec 12 04:47:23 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