Calcium in PDB 1y9i: Crystal Structure of Low Temperature Requirement C Protein From Listeria Monocytogenes

The structure of Crystal Structure of Low Temperature Requirement C Protein From Listeria Monocytogenes, PDB code: 1y9i was solved by D.Kumaran, S.Swaminathan, S.K.Burley, New York Sgx Research Center Forstructural Genomics (Nysgxrc), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 1.80
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	55.908, 101.069, 63.096, 90.00, 95.40, 90.00
R / Rfree (%)	21.1 / 24.5

The structure of Crystal Structure of Low Temperature Requirement C Protein From Listeria Monocytogenes also contains other interesting chemical elements:

Magnesium

(Mg)

4 atoms

The binding sites of Calcium atom in the Crystal Structure of Low Temperature Requirement C Protein From Listeria Monocytogenes (pdb code 1y9i). 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 Low Temperature Requirement C Protein From Listeria Monocytogenes, PDB code: 1y9i:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Crystal Structure of Low Temperature Requirement C Protein From Listeria Monocytogenes


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 Low Temperature Requirement C Protein From Listeria Monocytogenes within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca501 b:18.1 occ:1.00 O A:TYR95 2.4 16.7 1.0 O A:HOH694 2.4 19.2 1.0 OD1 A:ASP98 2.4 16.7 1.0 O A:HOH605 2.5 22.7 1.0 OE1 A:GLU99 2.5 20.5 1.0 O A:HOH611 2.5 22.4 1.0 OE2 A:GLU99 2.5 22.3 1.0 OD2 A:ASP98 2.7 20.5 1.0 CD A:GLU99 2.9 21.0 1.0 CG A:ASP98 2.9 19.4 1.0 C A:TYR95 3.6 17.8 1.0 CA A:GLY96 4.1 17.6 1.0 O A:HOH695 4.2 25.3 1.0 MG A:MG601 4.2 25.1 1.0 OD1 A:ASP91 4.2 25.7 1.0 O A:GLU92 4.3 22.7 1.0 N A:GLY96 4.3 17.1 1.0 CG A:GLU99 4.4 19.5 1.0 CB A:ASP98 4.4 16.8 1.0 O A:HOH651 4.6 37.2 1.0 CD2 A:TYR95 4.6 16.9 1.0 CA A:TYR95 4.7 17.8 1.0 O A:HOH606 4.7 28.4 1.0 O A:HOH711 4.8 40.1 1.0 C A:GLY96 4.8 18.2 1.0 O A:HOH635 4.8 31.1 1.0 CB A:TYR95 4.8 16.7 1.0 N A:GLU99 4.8 16.6 1.0 N A:ASP98 4.9 14.1 1.0 N A:TYR95 4.9 18.1 1.0 O A:GLY93 5.0 24.1 1.0

Calcium binding site 2 out of 4 in the Crystal Structure of Low Temperature Requirement C Protein From Listeria Monocytogenes


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 Low Temperature Requirement C Protein From Listeria Monocytogenes within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca502 b:15.1 occ:1.00 O B:HOH902 2.4 16.1 1.0 OD1 B:ASP98 2.4 18.2 1.0 O B:TYR95 2.4 13.3 1.0 O B:HOH827 2.5 19.8 1.0 OE2 B:GLU99 2.5 19.4 1.0 OE1 B:GLU99 2.5 20.2 1.0 O B:HOH834 2.5 23.7 1.0 OD2 B:ASP98 2.6 21.4 1.0 CD B:GLU99 2.9 19.2 1.0 CG B:ASP98 2.9 19.0 1.0 C B:TYR95 3.6 14.3 1.0 MG B:MG602 4.0 22.8 1.0 CA B:GLY96 4.1 13.8 1.0 OD1 B:ASP91 4.2 21.1 1.0 O B:GLU92 4.3 18.0 1.0 CG B:GLU99 4.4 19.5 1.0 N B:GLY96 4.4 14.3 1.0 CB B:ASP98 4.4 15.7 1.0 CD2 B:TYR95 4.6 16.6 1.0 O B:HOH833 4.7 27.7 1.0 N B:GLU99 4.7 12.6 1.0 CA B:TYR95 4.7 15.4 1.0 O B:HOH824 4.7 40.7 1.0 C B:GLY96 4.8 15.9 1.0 OD2 B:ASP145 4.8 33.3 1.0 CB B:TYR95 4.8 15.7 1.0 N B:ASP98 4.8 11.9 1.0 N B:TYR95 5.0 15.4 1.0 O B:GLY93 5.0 17.5 1.0

Calcium binding site 3 out of 4 in the Crystal Structure of Low Temperature Requirement C Protein From Listeria Monocytogenes


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 Low Temperature Requirement C Protein From Listeria Monocytogenes within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca503 b:18.8 occ:1.00 O C:TYR95 2.4 18.2 1.0 OD1 C:ASP98 2.4 17.7 1.0 OE2 C:GLU99 2.4 20.8 1.0 O C:HOH620 2.5 25.3 1.0 O C:HOH694 2.5 18.8 1.0 OE1 C:GLU99 2.5 18.7 1.0 OD2 C:ASP98 2.6 18.9 1.0 O C:HOH621 2.6 22.4 1.0 CG C:ASP98 2.8 18.2 1.0 CD C:GLU99 2.8 22.1 1.0 C C:TYR95 3.6 17.2 1.0 CA C:GLY96 4.1 14.9 1.0 MG C:MG603 4.2 27.1 1.0 OD1 C:ASP91 4.2 24.9 1.0 O C:GLU92 4.3 23.1 1.0 N C:GLY96 4.3 15.6 1.0 CB C:ASP98 4.3 14.2 1.0 CG C:GLU99 4.4 17.7 1.0 O C:HOH693 4.5 39.8 1.0 CD2 C:TYR95 4.6 15.9 1.0 CA C:TYR95 4.7 17.5 1.0 C C:GLY96 4.7 14.5 1.0 O C:HOH698 4.7 34.2 1.0 CB C:TYR95 4.8 17.9 1.0 N C:GLU99 4.8 14.5 1.0 N C:ASP98 4.8 14.6 1.0 O C:HOH612 4.9 39.0 1.0 OD2 C:ASP145 4.9 34.0 1.0 N C:TYR95 5.0 16.6 1.0

Calcium binding site 4 out of 4 in the Crystal Structure of Low Temperature Requirement C Protein From Listeria Monocytogenes


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 Low Temperature Requirement C Protein From Listeria Monocytogenes within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca504 b:22.5 occ:1.00 O D:HOH613 2.4 25.5 1.0 OD1 D:ASP98 2.4 20.1 1.0 O D:HOH615 2.4 18.6 1.0 O D:TYR95 2.4 19.0 1.0 O D:HOH612 2.5 23.2 1.0 OE1 D:GLU99 2.5 25.4 1.0 OD2 D:ASP98 2.6 20.2 1.0 OE2 D:GLU99 2.6 23.5 1.0 CG D:ASP98 2.8 20.0 1.0 CD D:GLU99 2.9 26.5 1.0 C D:TYR95 3.6 19.1 1.0 CA D:GLY96 4.1 18.2 1.0 O D:HOH680 4.2 38.0 1.0 MG D:MG604 4.2 27.8 1.0 OD1 D:ASP91 4.2 33.2 1.0 O D:GLU92 4.3 24.4 1.0 CB D:ASP98 4.3 18.9 1.0 O D:HOH673 4.4 44.0 1.0 N D:GLY96 4.4 18.3 1.0 CG D:GLU99 4.4 21.8 1.0 O D:HOH669 4.6 47.7 1.0 O D:HOH648 4.6 33.7 1.0 CD2 D:TYR95 4.6 15.0 1.0 CA D:TYR95 4.7 18.6 1.0 N D:GLU99 4.8 16.9 1.0 C D:GLY96 4.8 17.0 1.0 CB D:TYR95 4.8 18.2 1.0 N D:ASP98 4.8 17.1 1.0 OD2 D:ASP145 4.9 35.4 1.0 O D:HOH644 4.9 47.7 1.0 CG2 D:THR141 5.0 22.1 1.0

D.Kumaran, J.B.Bonanno, S.K.Burley, S.Swaminathan. Crystal Structure of Phosphatidylglycerophosphatase (Pgpase), A Putative Membrane-Bound Lipid Phosphatase, Reveals A Novel Binuclear Metal Binding Site and Two "Proton Wires". Proteins V. 64 851 2006.
ISSN: ISSN 0887-3585
PubMed: 16838328
DOI: 10.1002/PROT.21039