Calcium in PDB 2pvz: Crystal Structure of Methylaconitate Isomerase Prpf From Shewanella Oneidensis

The structure of Crystal Structure of Methylaconitate Isomerase Prpf From Shewanella Oneidensis, PDB code: 2pvz was solved by G.S.Garvey, I.R.Rayment, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	75.81 / 1.97
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	51.868, 104.058, 78.254, 90.00, 104.37, 90.00
R / Rfree (%)	15.8 / 18.8

The binding sites of Calcium atom in the Crystal Structure of Methylaconitate Isomerase Prpf From Shewanella Oneidensis (pdb code 2pvz). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Crystal Structure of Methylaconitate Isomerase Prpf From Shewanella Oneidensis, PDB code: 2pvz:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Crystal Structure of Methylaconitate Isomerase Prpf From Shewanella Oneidensis


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 Methylaconitate Isomerase Prpf From Shewanella Oneidensis within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1001 b:15.9 occ:1.00 O A:HOH1030 3.1 8.7 1.0 O A:HOH1183 3.2 26.7 1.0 NE2 A:GLN240 3.3 9.5 1.0 NZ B:LYS59 3.4 8.7 1.0 O A:HOH1403 3.6 34.4 1.0 CG2 A:THR68 3.8 6.8 1.0 CE B:LYS59 3.9 7.8 1.0 CB A:THR68 3.9 6.8 1.0 CB A:HIS318 3.9 8.5 1.0 CD B:LYS59 4.1 7.2 1.0 OE1 A:GLN240 4.2 9.9 1.0 CD A:GLN240 4.2 10.1 1.0 ND1 A:HIS318 4.2 10.8 1.0 OG1 A:THR68 4.3 7.2 1.0 CG A:HIS318 4.3 9.8 1.0 O B:HOH606 4.6 17.9 1.0 N A:HIS318 4.7 9.3 1.0 CA A:HIS318 4.8 9.2 1.0 O B:HOH466 4.9 9.8 1.0 O A:HOH1153 4.9 15.9 1.0 O A:HOH1109 4.9 17.9 1.0

Calcium binding site 2 out of 4 in the Crystal Structure of Methylaconitate Isomerase Prpf From Shewanella Oneidensis


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 Methylaconitate Isomerase Prpf From Shewanella Oneidensis within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1002 b:16.4 occ:1.00 O B:HOH658 3.1 25.1 1.0 O B:HOH671 3.2 30.9 1.0 O B:HOH405 3.2 7.0 1.0 NE2 B:GLN240 3.2 9.4 1.0 NZ A:LYS59 3.4 10.6 1.0 CG2 B:THR68 3.7 5.5 1.0 CE A:LYS59 3.8 8.5 1.0 CB B:THR68 3.9 6.3 1.0 CB B:HIS318 3.9 7.6 1.0 CD A:LYS59 4.0 7.1 1.0 CD B:GLN240 4.1 10.2 1.0 OE1 B:GLN240 4.1 10.6 1.0 CD2 B:HIS318 4.2 7.8 1.0 CG B:HIS318 4.3 7.9 1.0 OG1 B:THR68 4.3 6.6 1.0 N B:HIS318 4.7 7.6 1.0 O B:HOH476 4.8 11.4 1.0 O A:HOH1172 4.8 27.9 1.0 O B:HOH515 4.8 24.0 1.0 CA B:HIS318 4.9 7.5 1.0 O A:HOH1022 5.0 8.7 1.0

Calcium binding site 3 out of 4 in the Crystal Structure of Methylaconitate Isomerase Prpf From Shewanella Oneidensis


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 Methylaconitate Isomerase Prpf From Shewanella Oneidensis within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1003 b:23.5 occ:1.00 OG A:SER312 3.2 15.2 1.0 NZ A:LYS73 3.3 10.0 1.0 OG A:SER69 3.3 8.9 1.0 O A:HOH1251 3.3 33.2 1.0 CD2 A:HIS317 3.6 9.9 1.0 NE2 A:HIS317 3.7 10.7 1.0 C A:SER69 3.7 7.2 1.0 O A:SER69 3.7 7.2 1.0 CB A:SER69 3.7 7.3 1.0 N A:SER70 3.8 7.0 1.0 CB A:SER312 3.9 14.2 1.0 CA A:SER70 3.9 7.3 1.0 OG A:SER70 3.9 9.1 1.0 CE A:LYS73 4.0 8.2 1.0 CG A:MET321 4.0 12.3 1.0 C2 A:EDO1005 4.1 22.2 1.0 O2 A:EDO1005 4.1 23.8 1.0 CA A:SER69 4.4 7.5 1.0 CB A:SER70 4.5 7.3 1.0 OD1 A:CSD107 4.5 15.1 1.0 O A:HOH1250 4.7 17.8 1.0 OE1 A:GLN93 4.8 9.1 1.0 O A:HOH1183 4.9 26.7 1.0 OG A:SER22 4.9 7.7 1.0 CG A:HIS317 4.9 9.7 1.0 CE1 A:HIS317 5.0 11.1 1.0

Calcium binding site 4 out of 4 in the Crystal Structure of Methylaconitate Isomerase Prpf From Shewanella Oneidensis


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 Methylaconitate Isomerase Prpf From Shewanella Oneidensis within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1004 b:18.5 occ:1.00 O A:HOH1186 3.0 19.3 1.0 O A:HOH1364 3.1 14.8 1.0 NE2 A:GLN30 3.2 13.2 1.0 N A:GLN30 3.3 8.5 1.0 N A:LEU29 3.6 7.6 1.0 CG A:GLN30 3.7 9.8 1.0 CB A:GLN30 3.7 8.8 1.0 CB A:SER78 3.8 9.3 1.0 CB A:LEU29 3.9 8.2 1.0 CB A:ARG28 3.9 7.4 1.0 O A:LEU77 3.9 8.4 1.0 CA A:SER78 3.9 9.8 1.0 CD A:GLN30 3.9 12.2 1.0 CA A:LEU29 4.1 8.4 1.0 CA A:GLN30 4.1 8.7 1.0 C A:LEU29 4.2 8.3 1.0 C A:ARG28 4.2 7.7 1.0 CD2 A:LEU123 4.2 11.0 1.0 CA A:ARG28 4.3 7.2 1.0 CG A:ARG28 4.6 7.7 1.0 CD A:ARG28 4.6 7.4 1.0 N A:HIS79 4.7 11.7 1.0 C A:LEU77 4.8 8.2 1.0 O A:HOH1318 4.8 31.5 1.0 N A:SER78 4.9 8.5 1.0 O A:HOH1203 4.9 26.8 1.0 C A:SER78 4.9 10.6 1.0 CG A:LEU29 5.0 8.8 1.0

G.S.Garvey, C.J.Rocco, J.C.Escalante-Semerena, I.Rayment. The Three-Dimensional Crystal Structure of the Prpf Protein of Shewanella Oneidensis Complexed with Trans-Aconitate: Insights Into Its Biological Function. Protein Sci. V. 16 1274 2007.
ISSN: ISSN 0961-8368
PubMed: 17567742
DOI: 10.1110/PS.072801907