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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

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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

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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

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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

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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

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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

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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

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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

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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

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