Atomistry » Sodium » PDB 7bqj-7cdu » 7c90
Atomistry »
  Sodium »
    PDB 7bqj-7cdu »
      7c90 »

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

Protein crystallography data

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

Other elements in 7c90:

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
Calcium (Ca) 4 atoms

Sodium Binding Sites:

The binding sites of Sodium 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 Sodium atom.
In total 8 binding sites of Sodium where determined in the Crystal Structure of Cytochrome Cl From the Marine Methylotrophic Bacterium Methylophaga Aminisulfidivorans Mpt (Ma-Cytcl), PDB code: 7c90:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Sodium binding site 1 out of 8 in 7c90

Go back to Sodium Binding Sites List in 7c90
Sodium binding site 1 out of 8 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 Sodium with other atoms in the Na 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:Na207

b:23.6
occ:1.00
 O A:TYR108 2.5 28.4 1.0
O A:ASP106 2.6 30.8 1.0
O A:HOH310 2.6 42.5 1.0
O A:HOH321 2.7 40.0 1.0
OD1 A:ASP106 2.8 38.3 1.0
CE1 A:TYR109 3.0 30.2 1.0
CZ A:TYR109 3.2 31.7 1.0
CD1 A:TYR109 3.2 27.8 1.0
C A:ASP106 3.5 32.7 1.0
C A:TYR108 3.6 26.7 1.0
CE2 A:TYR109 3.7 30.6 1.0
CG A:TYR109 3.7 27.4 1.0
OH A:TYR109 3.8 30.7 1.0
CG A:ASP106 3.8 36.1 1.0
NA A:NA208 3.9 31.3 1.0
CD2 A:TYR109 3.9 30.9 1.0
N A:TYR108 4.0 30.7 1.0
N A:ASP106 4.1 29.3 1.0
CA A:ASP106 4.2 30.6 1.0
N A:ASP107 4.3 33.6 1.0
O A:LEU104 4.3 35.6 1.0
C A:ASP107 4.3 33.4 1.0
O A:ALA103 4.3 28.4 1.0
N A:TYR109 4.4 27.0 1.0
CA A:ASP107 4.4 38.4 1.0
C A:LEU104 4.4 32.5 1.0
CA A:TYR108 4.4 31.6 1.0
CA A:TYR109 4.4 25.4 1.0
OD2 A:ASP106 4.6 44.2 1.0
CB A:ASP106 4.6 36.6 1.0
CA A:LEU104 4.7 30.4 1.0
CB A:TYR109 4.7 24.7 1.0
O2A A:HEC201 4.9 29.1 1.0
N A:GLY105 4.9 32.7 1.0

Sodium binding site 2 out of 8 in 7c90

Go back to Sodium Binding Sites List in 7c90
Sodium binding site 2 out of 8 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 Sodium with other atoms in the Na 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
A:Na208

b:31.3
occ:1.00
 O A:HOH365 2.5 37.4 1.0
O A:TYR108 2.6 28.4 1.0
O B:HOH362 2.8 48.2 1.0
OD1 A:ASP106 2.8 38.3 1.0
OD2 A:ASP106 2.9 44.2 1.0
O A:HOH321 2.9 40.0 1.0
O A:ALA103 2.9 28.4 1.0
CG A:ASP106 3.2 36.1 1.0
C A:TYR108 3.4 26.7 1.0
NA A:NA207 3.9 23.6 1.0
C A:ALA103 4.0 26.9 1.0
CB A:TYR108 4.0 35.3 1.0
CB A:PRO102 4.0 30.4 1.0
O A:HOH342 4.1 42.3 1.0
O2A A:HEC201 4.1 29.1 1.0
N A:TYR109 4.2 27.0 1.0
CA A:TYR108 4.2 31.6 1.0
N A:ALA103 4.3 29.1 1.0
CB A:ALA103 4.4 32.0 1.0
CA A:TYR109 4.4 25.4 1.0
CA A:ALA103 4.5 29.0 1.0
N A:TYR108 4.7 30.7 1.0
CB A:ASP106 4.7 36.6 1.0
C A:PRO102 4.9 28.0 1.0

Sodium binding site 3 out of 8 in 7c90

Go back to Sodium Binding Sites List in 7c90
Sodium binding site 3 out of 8 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 Sodium with other atoms in the Na 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
B:Na207

b:18.8
occ:1.00
 O B:HOH354 2.7 27.8 1.0
OD2 B:ASP106 2.7 42.9 1.0
O B:TYR108 2.8 31.2 1.0
OD1 B:ASP106 2.9 37.4 1.0
O B:HOH316 2.9 31.0 1.0
O A:HOH335 3.0 34.2 1.0
O B:ALA103 3.0 22.4 1.0
CG B:ASP106 3.2 37.5 1.0
C B:TYR108 3.8 29.0 1.0
NA B:NA208 3.8 17.9 1.0
C B:ALA103 4.0 25.4 1.0
CD2 B:TYR108 4.1 26.4 1.0
CB B:PRO102 4.1 28.2 1.0
O1A B:HEC201 4.2 28.7 1.0
CB B:ALA103 4.3 26.8 1.0
O B:HOH365 4.4 28.6 1.0
N B:ALA103 4.4 26.6 1.0
CA B:ALA103 4.5 25.6 1.0
CB B:TYR108 4.5 27.1 1.0
N B:TYR109 4.5 27.9 1.0
CA B:TYR109 4.6 27.4 1.0
CA B:TYR108 4.6 29.5 1.0
CB B:ASP106 4.7 31.1 1.0
O A:THR110 4.7 24.2 1.0
CG B:TYR108 4.8 27.0 1.0
C B:PRO102 4.9 28.4 1.0
N B:TYR108 4.9 30.7 1.0
CE2 B:TYR108 5.0 28.2 1.0

Sodium binding site 4 out of 8 in 7c90

Go back to Sodium Binding Sites List in 7c90
Sodium binding site 4 out of 8 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 Sodium with other atoms in the Na 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
B:Na208

b:17.9
occ:1.00
 O B:TYR108 2.6 31.2 1.0
O B:HOH316 2.7 31.0 1.0
OD1 B:ASP106 2.7 37.4 1.0
O B:ASP106 2.7 29.0 1.0
CE2 B:TYR109 3.2 27.3 1.0
CD2 B:TYR109 3.3 28.9 1.0
CZ B:TYR109 3.5 33.2 1.0
C B:ASP106 3.6 29.0 1.0
C B:TYR108 3.6 29.0 1.0
CG B:TYR109 3.6 28.3 1.0
CG B:ASP106 3.7 37.5 1.0
O B:LEU104 3.8 33.2 1.0
CE1 B:TYR109 3.8 33.8 1.0
NA B:NA207 3.8 18.8 1.0
CD1 B:TYR109 3.9 31.1 1.0
N B:ASP106 4.1 27.8 1.0
C B:LEU104 4.1 26.7 1.0
O B:ALA103 4.1 22.4 1.0
N B:TYR108 4.2 30.7 1.0
OH B:TYR109 4.2 30.1 1.0
CA B:TYR109 4.3 27.4 1.0
N B:TYR109 4.3 27.9 1.0
CA B:ASP106 4.3 30.6 1.0
N B:ASP107 4.3 29.8 1.0
CA B:LEU104 4.4 25.8 1.0
OD2 B:ASP106 4.4 42.9 1.0
C B:ASP107 4.4 32.7 1.0
CB B:TYR109 4.5 29.5 1.0
CA B:ASP107 4.5 34.4 1.0
CA B:TYR108 4.6 29.5 1.0
CB B:ASP106 4.6 31.1 1.0
O1A B:HEC201 4.8 28.7 1.0
N B:GLY105 4.8 27.7 1.0
C B:ALA103 4.9 25.4 1.0
C B:GLY105 4.9 28.9 1.0

Sodium binding site 5 out of 8 in 7c90

Go back to Sodium Binding Sites List in 7c90
Sodium binding site 5 out of 8 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 Sodium with other atoms in the Na binding site number 5 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:Na205

b:28.6
occ:1.00
 O C:ASP106 2.7 33.1 1.0
O C:TYR108 2.7 29.7 1.0
O C:HOH322 2.7 70.0 1.0
O C:HOH324 2.8 41.4 1.0
OD1 C:ASP106 2.8 46.0 1.0
CE2 C:TYR109 3.2 29.7 1.0
NA C:NA206 3.4 31.6 1.0
CZ C:TYR109 3.4 33.9 1.0
C C:ASP106 3.5 30.3 1.0
CD2 C:TYR109 3.5 29.2 1.0
C C:TYR108 3.7 31.6 1.0
CE1 C:TYR109 3.9 34.6 1.0
CG C:TYR109 3.9 27.5 1.0
CG C:ASP106 3.9 37.6 1.0
N C:TYR108 3.9 34.4 1.0
OH C:TYR109 4.0 34.0 1.0
CD1 C:TYR109 4.0 31.6 1.0
N C:ASP106 4.1 31.8 1.0
O C:ALA103 4.1 27.7 1.0
N C:ASP107 4.2 32.8 1.0
O C:LEU104 4.2 35.3 1.0
CA C:ASP106 4.3 33.4 1.0
CA C:ASP107 4.3 39.4 1.0
C C:LEU104 4.4 34.6 1.0
C C:ASP107 4.4 38.2 1.0
N C:TYR109 4.5 27.9 1.0
CA C:TYR108 4.5 33.4 1.0
CA C:LEU104 4.5 32.0 1.0
CA C:TYR109 4.6 28.0 1.0
CB C:ASP106 4.7 36.1 1.0
O1A C:HEC201 4.8 29.7 1.0
OD2 C:ASP106 4.8 45.6 1.0
CB C:TYR109 4.8 28.0 1.0
N C:GLY105 4.9 37.0 1.0
C C:ALA103 5.0 29.8 1.0

Sodium binding site 6 out of 8 in 7c90

Go back to Sodium Binding Sites List in 7c90
Sodium binding site 6 out of 8 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 Sodium with other atoms in the Na binding site number 6 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:Na206

b:31.6
occ:1.00
 O C:TYR108 2.5 29.7 1.0
O C:HOH324 2.6 41.4 1.0
OD1 C:ASP106 2.6 46.0 1.0
O C:ALA103 2.7 27.7 1.0
O C:HOH323 2.7 45.5 1.0
O C:HOH355 2.7 40.2 1.0
OD2 C:ASP106 3.2 45.6 1.0
CG C:ASP106 3.3 37.6 1.0
NA C:NA205 3.4 28.6 1.0
C C:TYR108 3.6 31.6 1.0
O D:HOH341 3.8 36.0 1.0
C C:ALA103 3.8 29.8 1.0
CB C:PRO102 4.1 28.9 1.0
O1A C:HEC201 4.1 29.7 1.0
CB C:TYR108 4.3 40.4 1.0
N C:ALA103 4.3 28.4 1.0
CA C:TYR108 4.4 33.4 1.0
CA C:ALA103 4.4 28.9 1.0
CB C:ALA103 4.5 32.3 1.0
N C:TYR109 4.5 27.9 1.0
O C:HOH343 4.6 34.9 1.0
N C:TYR108 4.6 34.4 1.0
CA C:TYR109 4.6 28.0 1.0
C C:PRO102 4.8 27.3 1.0
CB C:ASP106 4.8 36.1 1.0
N C:LEU104 4.8 29.7 1.0
CG C:PRO102 4.9 29.8 1.0
O D:HOH304 4.9 78.1 1.0

Sodium binding site 7 out of 8 in 7c90

Go back to Sodium Binding Sites List in 7c90
Sodium binding site 7 out of 8 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 Sodium with other atoms in the Na binding site number 7 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:Na204

b:21.8
occ:1.00
 O D:HOH362 2.6 30.1 1.0
O D:HOH327 2.7 36.0 1.0
OD2 D:ASP106 2.7 41.0 1.0
O D:TYR108 2.8 30.9 1.0
O C:HOH325 2.8 47.3 1.0
OD1 D:ASP106 3.0 36.6 1.0
O D:ALA103 3.1 34.4 1.0
CG D:ASP106 3.2 43.3 1.0
C D:TYR108 3.8 32.5 1.0
NA D:NA205 3.9 24.8 1.0
C D:ALA103 4.1 30.5 1.0
CD2 D:TYR108 4.1 38.3 1.0
CB D:PRO102 4.2 31.2 1.0
O D:HOH358 4.2 35.8 1.0
O D:HOH377 4.3 63.6 1.0
O1A D:HEC201 4.3 31.5 1.0
N D:ALA103 4.4 29.2 1.0
CB D:TYR108 4.5 36.6 1.0
CB D:ALA103 4.5 34.7 1.0
O C:THR110 4.6 26.4 1.0
CA D:TYR108 4.6 34.2 1.0
N D:TYR109 4.6 29.6 1.0
CA D:ALA103 4.6 32.2 1.0
CA D:TYR109 4.7 33.1 1.0
CB D:ASP106 4.7 37.7 1.0
CG D:TYR108 4.8 37.5 1.0
N D:TYR108 4.9 32.9 1.0
C D:PRO102 4.9 28.6 1.0

Sodium binding site 8 out of 8 in 7c90

Go back to Sodium Binding Sites List in 7c90
Sodium binding site 8 out of 8 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 Sodium with other atoms in the Na binding site number 8 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:Na205

b:24.8
occ:1.00
 O D:ASP106 2.5 38.2 1.0
OD1 D:ASP106 2.5 36.6 1.0
O D:TYR108 2.7 30.9 1.0
O D:HOH327 2.8 36.0 1.0
CE2 D:TYR109 3.3 31.1 1.0
CD2 D:TYR109 3.4 32.5 1.0
C D:ASP106 3.4 38.5 1.0
CZ D:TYR109 3.5 32.0 1.0
CG D:ASP106 3.6 43.3 1.0
C D:TYR108 3.7 32.5 1.0
O D:LEU104 3.8 46.4 1.0
CG D:TYR109 3.8 31.6 1.0
CE1 D:TYR109 3.9 31.7 1.0
NA D:NA204 3.9 21.8 1.0
N D:ASP106 4.0 39.9 1.0
CD1 D:TYR109 4.0 32.9 1.0
C D:LEU104 4.1 36.9 1.0
O D:ALA103 4.1 34.4 1.0
OH D:TYR109 4.1 29.7 1.0
CA D:ASP106 4.2 40.2 1.0
N D:TYR108 4.2 32.9 1.0
N D:ASP107 4.3 35.9 1.0
CA D:LEU104 4.3 32.6 1.0
OD2 D:ASP106 4.4 41.0 1.0
N D:TYR109 4.5 29.6 1.0
CA D:TYR109 4.5 33.1 1.0
CB D:ASP106 4.5 37.7 1.0
CA D:ASP107 4.5 37.6 1.0
C D:ASP107 4.5 35.3 1.0
CA D:TYR108 4.6 34.2 1.0
CB D:TYR109 4.7 34.6 1.0
N D:GLY105 4.7 39.0 1.0
O D:HOH318 4.8 37.0 1.0
C D:GLY105 4.8 38.9 1.0
C D:ALA103 4.9 30.5 1.0

Reference:

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
Page generated: Tue Oct 8 16:19:58 2024

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy