Calcium in PDB 7c90: Crystal Structure of Cytochrome Cl From the Marine Methylotrophic Bacterium Methylophaga Aminisulfidivorans Mpt (Ma-Cytcl)

The structure of Crystal Structure of Cytochrome Cl From the Marine Methylotrophic Bacterium Methylophaga Aminisulfidivorans Mpt (Ma-Cytcl), PDB code: 7c90 was solved by S.Ghosh, I.Dhanasingh, S.H.Lee, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.58 / 2.13
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	61.760, 76.060, 66.440, 90.00, 106.85, 90.00
R / Rfree (%)	14.8 / 20

The structure of Crystal Structure of Cytochrome Cl From the Marine Methylotrophic Bacterium Methylophaga Aminisulfidivorans Mpt (Ma-Cytcl) also contains other interesting chemical elements:

Iron	(Fe)	8 atoms
Sodium	(Na)	8 atoms

The binding sites of Calcium atom in the Crystal Structure of Cytochrome Cl From the Marine Methylotrophic Bacterium Methylophaga Aminisulfidivorans Mpt (Ma-Cytcl) (pdb code 7c90). 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 Cytochrome Cl From the Marine Methylotrophic Bacterium Methylophaga Aminisulfidivorans Mpt (Ma-Cytcl), PDB code: 7c90:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Crystal Structure of Cytochrome Cl From the Marine Methylotrophic Bacterium Methylophaga Aminisulfidivorans Mpt (Ma-Cytcl)


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 Cytochrome Cl From the Marine Methylotrophic Bacterium Methylophaga Aminisulfidivorans Mpt (Ma-Cytcl) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca205 b:61.8 occ:1.00 CD A:PRO112 3.6 26.3 1.0 CG A:LYS113 3.7 26.5 1.0 N A:LYS113 3.7 26.6 1.0 CG A:PRO112 3.8 26.0 1.0 CB A:LYS113 3.8 25.4 1.0 CD A:LYS113 3.9 30.8 1.0 N A:PRO112 4.0 24.6 1.0 O2 A:GOL203 4.1 73.3 1.0 CB A:TYR111 4.2 24.7 1.0 C A:TYR111 4.3 24.9 1.0 CA A:LYS113 4.4 26.2 1.0 CA A:TYR111 4.4 24.7 1.0 C2 A:GOL203 4.5 78.3 1.0 C3 A:GOL203 4.6 72.6 1.0 C A:PRO112 4.6 25.8 1.0 CA A:PRO112 4.7 25.4 1.0 CB A:PRO112 4.8 26.3 1.0

Calcium binding site 2 out of 4 in the Crystal Structure of Cytochrome Cl From the Marine Methylotrophic Bacterium Methylophaga Aminisulfidivorans Mpt (Ma-Cytcl)


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 Cytochrome Cl From the Marine Methylotrophic Bacterium Methylophaga Aminisulfidivorans Mpt (Ma-Cytcl) within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca205 b:64.8 occ:1.00 O A:HOH395 1.8 54.3 1.0 N B:LYS113 3.7 27.4 1.0 CD B:PRO112 3.7 29.6 1.0 CG B:LYS113 3.9 33.9 1.0 N B:PRO112 3.9 27.8 1.0 CB B:LYS113 3.9 28.6 1.0 CG B:PRO112 4.0 33.6 1.0 C B:TYR111 4.1 27.6 1.0 CD B:LYS113 4.2 36.1 1.0 CA B:TYR111 4.3 28.1 1.0 CB B:TYR111 4.4 27.5 1.0 CA B:LYS113 4.4 30.2 1.0 C B:PRO112 4.6 27.3 1.0 CA B:PRO112 4.6 29.0 1.0 O B:TYR111 4.8 28.3 1.0 CB B:PRO112 4.8 31.8 1.0

Calcium binding site 3 out of 4 in the Crystal Structure of Cytochrome Cl From the Marine Methylotrophic Bacterium Methylophaga Aminisulfidivorans Mpt (Ma-Cytcl)


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 Cytochrome Cl From the Marine Methylotrophic Bacterium Methylophaga Aminisulfidivorans Mpt (Ma-Cytcl) within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca203 b:66.4 occ:1.00 O C:HOH350 2.8 68.9 1.0 CD C:PRO112 3.5 27.6 1.0 CG C:PRO112 3.5 31.4 1.0 N C:LYS113 3.6 31.9 1.0 CG C:LYS113 3.6 33.3 1.0 CB C:LYS113 3.7 31.7 1.0 CD C:LYS113 3.8 34.8 1.0 N C:PRO112 3.8 27.8 1.0 O C:HOH383 4.1 60.2 1.0 CB C:TYR111 4.2 29.7 1.0 C C:TYR111 4.2 26.8 1.0 CA C:LYS113 4.3 31.2 1.0 CA C:TYR111 4.3 27.6 1.0 C C:PRO112 4.5 30.1 1.0 CA C:PRO112 4.5 29.0 1.0 CB C:PRO112 4.6 30.1 1.0 CE C:LYS113 4.9 32.8 1.0 CD1 C:TYR111 5.0 28.7 1.0 O C:TYR111 5.0 25.0 1.0

Calcium binding site 4 out of 4 in the Crystal Structure of Cytochrome Cl From the Marine Methylotrophic Bacterium Methylophaga Aminisulfidivorans Mpt (Ma-Cytcl)


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 Cytochrome Cl From the Marine Methylotrophic Bacterium Methylophaga Aminisulfidivorans Mpt (Ma-Cytcl) within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca202 b:66.2 occ:1.00 CD D:PRO112 3.4 32.4 1.0 N D:PRO112 3.9 29.9 1.0 N D:LYS113 3.9 31.1 1.0 CG D:LYS113 4.1 30.4 1.0 CB D:LYS113 4.1 30.1 1.0 CA D:TYR111 4.3 27.6 1.0 C D:TYR111 4.3 26.7 1.0 CB D:TYR111 4.3 28.4 1.0 CG D:PRO112 4.4 35.5 1.0 CD D:LYS113 4.6 32.8 1.0 CA D:LYS113 4.7 30.8 1.0 CA D:PRO112 4.7 31.0 1.0 CB D:PRO112 4.7 33.8 1.0 C D:PRO112 4.8 29.1 1.0 CD1 D:TYR111 5.0 26.9 1.0

S.Ghosh, I.Dhanasingh, J.Ryu, S.W.Kim, S.H.Lee. Crystal Structure of Cytochromeclfrom the Aquatic Methylotrophic Bacteriummethylophaga Aminisulfidivoransmpt. J Microbiol Biotechnol. V. 30 1261 2020.
ISSN: ESSN 1738-8872
PubMed: 32627749
DOI: 10.4014/JMB.2006.06029