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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: Sun Jul 14 07:00:07 2024

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