Magnesium 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:

Calcium

(Ca)

4 atoms

The binding sites of Magnesium 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 Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Crystal Structure of Low Temperature Requirement C Protein From Listeria Monocytogenes, PDB code: 1y9i:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium 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 Magnesium with other atoms in the Mg 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:Mg601 b:25.1 occ:1.00 O A:HOH606 2.0 28.4 1.0 OD2 A:ASP98 2.0 20.5 1.0 O A:THR141 2.0 17.2 1.0 O A:HOH695 2.1 25.3 1.0 OD2 A:ASP145 2.1 30.2 1.0 OD1 A:ASP144 2.5 30.0 1.0 CG A:ASP98 3.1 19.4 1.0 CG A:ASP145 3.1 27.2 1.0 C A:THR141 3.2 17.9 1.0 CG A:ASP144 3.3 26.8 1.0 O A:HOH611 3.4 22.4 1.0 OD2 A:ASP144 3.4 31.5 1.0 OD1 A:ASP145 3.5 26.9 1.0 CB A:ASP98 3.6 16.8 1.0 CA A:THR141 3.8 18.1 1.0 O A:HOH692 4.0 35.7 1.0 CG2 A:THR141 4.1 17.4 1.0 OD1 A:ASP91 4.2 25.7 1.0 OD1 A:ASP98 4.2 16.7 1.0 CA A:CA501 4.2 18.1 1.0 N A:PHE142 4.3 17.6 1.0 CB A:ASP145 4.4 21.5 1.0 N A:ASP145 4.4 20.2 1.0 OE2 A:GLU99 4.4 22.3 1.0 O A:HIS140 4.6 22.2 1.0 CA A:PHE142 4.6 17.6 1.0 CB A:THR141 4.6 21.1 1.0 O A:HOH694 4.7 19.2 1.0 CB A:ASP144 4.7 24.1 1.0 OD2 A:ASP91 4.8 27.7 1.0 CD A:GLU99 4.8 21.0 1.0 CG A:ASP91 4.8 26.8 1.0 O A:HOH651 4.8 37.2 1.0 CA A:ASP145 4.9 21.0 1.0 O A:HOH676 5.0 44.6 1.0 CA A:ASP98 5.0 15.5 1.0 N A:THR141 5.0 20.2 1.0

Magnesium 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 Magnesium with other atoms in the Mg 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:Mg602 b:22.8 occ:1.00 O B:HOH823 2.1 37.3 1.0 OD2 B:ASP98 2.1 21.4 1.0 OD2 B:ASP145 2.1 33.3 1.0 O B:THR141 2.3 16.3 1.0 OD1 B:ASP144 2.5 33.2 1.0 O B:HOH827 3.1 19.8 1.0 CG B:ASP98 3.3 19.0 1.0 CG B:ASP145 3.3 25.1 1.0 C B:THR141 3.5 14.6 1.0 CG B:ASP144 3.5 30.9 1.0 O B:HOH922 3.7 38.1 1.0 OD2 B:ASP144 3.8 37.5 1.0 OD1 B:ASP91 3.9 21.1 1.0 CB B:ASP98 3.9 15.7 1.0 OD1 B:ASP145 3.9 31.4 1.0 CA B:CA502 4.0 15.1 1.0 CA B:THR141 4.0 14.2 1.0 OD1 B:ASP98 4.2 18.2 1.0 CG2 B:THR141 4.3 14.8 1.0 OE2 B:GLU99 4.3 19.4 1.0 CB B:ASP145 4.4 20.5 1.0 OD2 B:ASP91 4.4 23.6 1.0 N B:ASP145 4.5 14.9 1.0 O B:HOH824 4.5 40.7 1.0 CG B:ASP91 4.5 23.7 1.0 N B:PHE142 4.6 12.0 1.0 O B:HOH902 4.7 16.1 1.0 O B:HIS140 4.8 18.3 1.0 CD B:GLU99 4.8 19.2 1.0 CB B:THR141 4.8 14.5 1.0 CB B:ASP144 4.8 25.2 1.0 CA B:PHE142 4.9 14.3 1.0

Magnesium 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 Magnesium with other atoms in the Mg 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:Mg603 b:27.1 occ:1.00 O C:HOH612 1.9 39.0 1.0 OD2 C:ASP145 2.0 34.0 1.0 O C:THR141 2.1 16.4 1.0 OD2 C:ASP98 2.2 18.9 1.0 OD1 C:ASP144 2.5 33.2 1.0 O C:HOH621 3.2 22.4 1.0 C C:THR141 3.2 16.1 1.0 CG C:ASP98 3.3 18.2 1.0 CG C:ASP145 3.3 28.3 1.0 CG C:ASP144 3.4 30.6 1.0 OD2 C:ASP144 3.5 37.4 1.0 CB C:ASP98 3.8 14.2 1.0 O C:HOH613 3.8 39.8 1.0 CA C:THR141 3.8 16.4 1.0 OD1 C:ASP91 3.9 24.9 1.0 OD1 C:ASP145 4.0 29.3 1.0 CG2 C:THR141 4.1 15.8 1.0 CA C:CA503 4.2 18.8 1.0 OD1 C:ASP98 4.3 17.7 1.0 OE2 C:GLU99 4.3 20.8 1.0 CB C:ASP145 4.3 21.8 1.0 N C:PHE142 4.4 15.5 1.0 N C:ASP145 4.5 17.6 1.0 OD2 C:ASP91 4.6 28.1 1.0 CG C:ASP91 4.6 27.8 1.0 CB C:THR141 4.6 18.3 1.0 O C:HIS140 4.6 19.1 1.0 O C:HOH692 4.6 46.5 1.0 CA C:PHE142 4.7 17.4 1.0 O C:HOH694 4.7 18.8 1.0 CB C:ASP144 4.8 25.4 1.0 CD C:GLU99 4.9 22.1 1.0

Magnesium 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 Magnesium with other atoms in the Mg 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:Mg604 b:27.8 occ:1.00 OD2 D:ASP145 2.0 35.4 1.0 O D:HOH669 2.0 47.7 1.0 O D:HOH680 2.0 38.0 1.0 O D:THR141 2.1 22.3 1.0 OD2 D:ASP98 2.1 20.2 1.0 OD1 D:ASP144 2.4 38.1 1.0 CG D:ASP145 3.1 32.2 1.0 CG D:ASP98 3.1 20.0 1.0 C D:THR141 3.2 20.5 1.0 CG D:ASP144 3.2 35.9 1.0 OD2 D:ASP144 3.2 41.2 1.0 O D:HOH612 3.3 23.2 1.0 OD1 D:ASP145 3.6 33.0 1.0 CB D:ASP98 3.6 18.9 1.0 CA D:THR141 3.8 21.9 1.0 O D:HOH665 3.9 30.0 1.0 CG2 D:THR141 4.0 22.1 1.0 OD1 D:ASP91 4.1 33.2 1.0 CA D:CA504 4.2 22.5 1.0 OD1 D:ASP98 4.2 20.1 1.0 CB D:ASP145 4.3 26.9 1.0 N D:PHE142 4.3 18.4 1.0 N D:ASP145 4.4 24.5 1.0 O D:HOH666 4.4 44.3 1.0 OE2 D:GLU99 4.5 23.5 1.0 CB D:THR141 4.5 22.2 1.0 CA D:PHE142 4.6 19.4 1.0 O D:HIS140 4.6 22.4 1.0 CB D:ASP144 4.6 29.5 1.0 CD D:GLU99 4.8 26.5 1.0 O D:HOH615 4.8 18.6 1.0 OD2 D:ASP91 4.8 33.3 1.0 CG D:ASP91 4.8 32.7 1.0 OE1 D:GLU99 4.9 25.4 1.0 CA D:ASP145 4.9 23.5 1.0 CA D:ASP98 5.0 16.8 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