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Sodium in PDB 9mva: Mycobacterium Abscessus EIS2 in Complex with Non-Hydrolyzable Coenzymea

Protein crystallography data

The structure of Mycobacterium Abscessus EIS2 in Complex with Non-Hydrolyzable Coenzymea, PDB code: 9mva was solved by T.D.Jayasinghe, A.L.Coker, T.Rajendra, D.Miller, R.E.Lee, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 34.36 / 1.80
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 195.695, 209.587, 152.291, 90, 90, 90
R / Rfree (%) 19.1 / 22.2

Other elements in 9mva:

The structure of Mycobacterium Abscessus EIS2 in Complex with Non-Hydrolyzable Coenzymea also contains other interesting chemical elements:

Chlorine (Cl) 6 atoms

Sodium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 14;

Binding sites:

The binding sites of Sodium atom in the Mycobacterium Abscessus EIS2 in Complex with Non-Hydrolyzable Coenzymea (pdb code 9mva). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 14 binding sites of Sodium where determined in the Mycobacterium Abscessus EIS2 in Complex with Non-Hydrolyzable Coenzymea, PDB code: 9mva:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Sodium binding site 1 out of 14 in 9mva

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Sodium binding site 1 out of 14 in the Mycobacterium Abscessus EIS2 in Complex with Non-Hydrolyzable Coenzymea


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Mycobacterium Abscessus EIS2 in Complex with Non-Hydrolyzable Coenzymea within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na507

b:32.2
occ:1.00
 O A:HOH960 2.1 26.8 1.0
O A:HOH815 2.1 33.1 1.0
O A:HOH879 2.2 30.0 1.0
O A:HOH643 2.2 31.6 1.0
O A:GLY275 2.6 27.5 1.0
O A:HOH645 2.7 24.5 1.0
O A:HOH797 2.7 31.5 1.0
C A:GLY275 3.5 26.3 1.0
O A:HOH787 3.9 32.2 1.0
O A:HOH639 3.9 25.2 1.0
CA A:GLY275 4.0 19.4 1.0
O A:HIS274 4.1 17.4 0.8
O A:ALA407 4.1 14.1 1.0
O A:HOH607 4.1 26.2 1.0
O A:GLN245 4.4 16.1 1.0
N A:ALA276 4.5 19.5 1.0
OH A:TYR273 4.5 20.1 1.0
O A:HOH974 4.7 39.3 1.0
O A:HOH998 4.7 32.9 1.0
CE1 A:TYR273 4.8 18.1 1.0
CA A:ALA276 4.9 15.8 1.0
CZ A:TYR273 5.0 18.0 1.0
C A:HIS274 5.0 16.8 0.8
N A:GLY275 5.0 22.5 1.0

Sodium binding site 2 out of 14 in 9mva

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Sodium binding site 2 out of 14 in the Mycobacterium Abscessus EIS2 in Complex with Non-Hydrolyzable Coenzymea


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Mycobacterium Abscessus EIS2 in Complex with Non-Hydrolyzable Coenzymea within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na508

b:36.5
occ:1.00
 O A:HOH982 2.2 33.7 1.0
O A:HOH640 2.2 28.6 1.0
O A:HOH1043 2.3 29.5 1.0
O A:HOH1022 2.4 26.5 1.0
O A:HOH641 3.9 31.1 1.0
O A:HOH862 4.3 21.2 1.0
O A:HOH821 4.5 30.4 1.0
O A:VAL177 4.5 19.3 1.0
O A:HOH962 4.6 29.9 1.0
CG1 A:VAL177 4.7 21.8 1.0

Sodium binding site 3 out of 14 in 9mva

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Sodium binding site 3 out of 14 in the Mycobacterium Abscessus EIS2 in Complex with Non-Hydrolyzable Coenzymea


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Mycobacterium Abscessus EIS2 in Complex with Non-Hydrolyzable Coenzymea within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na509

b:20.0
occ:1.00
 OE2 B:GLU120 2.7 15.8 1.0
N C:LEU267 2.8 11.0 1.0
O C:HOH797 2.9 15.9 1.0
NH1 C:ARG269 2.9 10.5 1.0
CD B:GLU120 3.3 12.7 1.0
OE1 B:GLU120 3.4 11.6 1.0
NH2 C:ARG143 3.5 19.5 1.0
CA C:LEU267 3.5 13.0 1.0
O B:HOH685 3.6 16.0 1.0
NH2 C:ARG269 3.7 13.8 1.0
C C:ASP266 3.8 11.8 1.0
CA C:ASP266 3.8 13.3 1.0
CZ C:ARG269 3.8 14.4 1.0
O C:HOH824 4.0 19.1 1.0
CB C:ASP266 4.2 12.9 1.0
O B:HOH679 4.3 13.5 1.0
OD1 C:ASP266 4.3 15.0 1.0
C C:LEU267 4.3 11.7 1.0
CG C:PRO238 4.4 11.1 1.0
N6 B:SOP502 4.5 17.9 1.0
CZ C:ARG143 4.6 26.1 1.0
N C:VAL268 4.6 12.3 1.0
CD2 C:LEU267 4.7 13.0 1.0
CG B:GLU120 4.7 12.3 1.0
CG C:ASP266 4.8 14.7 1.0
CB C:LEU267 4.8 13.4 1.0
O C:VAL268 4.8 10.7 1.0
O C:ASP266 4.9 11.6 1.0
O C:MET265 5.0 15.5 1.0

Sodium binding site 4 out of 14 in 9mva

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Sodium binding site 4 out of 14 in the Mycobacterium Abscessus EIS2 in Complex with Non-Hydrolyzable Coenzymea


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Mycobacterium Abscessus EIS2 in Complex with Non-Hydrolyzable Coenzymea within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na510

b:29.6
occ:1.00
 O B:HOH956 2.1 21.5 1.0
O B:HOH845 2.2 30.2 1.0
O B:HOH831 2.2 27.8 1.0
O B:HOH726 2.2 24.7 1.0
O B:HOH621 2.9 22.9 1.0
O B:GLY275 2.9 22.9 1.0
C B:GLY275 3.6 25.1 1.0
O B:HOH716 3.8 25.6 1.0
O B:HOH775 4.0 32.3 1.0
CA B:GLY275 4.0 15.6 1.0
O B:ALA407 4.1 13.6 1.0
O B:HOH601 4.1 24.4 1.0
O B:HIS274 4.1 18.5 1.0
O B:GLN245 4.3 15.7 1.0
N B:ALA276 4.5 15.5 1.0
OH B:TYR273 4.6 20.0 1.0
O B:HOH1012 4.8 30.3 1.0
O B:HOH980 4.8 38.5 1.0
CE1 B:TYR273 4.9 15.8 1.0
CA B:ALA276 4.9 12.9 1.0
CH2 B:TRP195 4.9 13.7 1.0
C B:HIS274 5.0 16.8 1.0
O B:PRO408 5.0 12.7 1.0

Sodium binding site 5 out of 14 in 9mva

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Sodium binding site 5 out of 14 in the Mycobacterium Abscessus EIS2 in Complex with Non-Hydrolyzable Coenzymea


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Mycobacterium Abscessus EIS2 in Complex with Non-Hydrolyzable Coenzymea within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na511

b:36.8
occ:1.00
 O B:HOH605 2.0 27.9 1.0
O B:HOH988 2.2 32.4 1.0
O B:HOH1024 2.2 31.2 1.0
O B:HOH1049 2.2 34.3 1.0
O B:HOH948 3.8 34.8 1.0
O B:HOH844 4.2 21.3 1.0
O B:VAL177 4.3 20.5 1.0
O B:HOH700 4.3 31.0 1.0
O B:HOH919 4.5 28.4 1.0
CG1 B:VAL177 4.6 21.0 1.0
CA B:GLY180 4.7 16.0 1.0
CA B:VAL177 5.0 19.8 1.0

Sodium binding site 6 out of 14 in 9mva

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Sodium binding site 6 out of 14 in the Mycobacterium Abscessus EIS2 in Complex with Non-Hydrolyzable Coenzymea


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Mycobacterium Abscessus EIS2 in Complex with Non-Hydrolyzable Coenzymea within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na508

b:25.1
occ:1.00
 O C:HOH620 2.1 23.3 1.0
O C:HOH1015 2.2 23.2 1.0
O C:HOH1063 2.2 26.2 1.0
O C:HOH1050 2.2 22.3 1.0
O C:HOH775 4.1 13.8 1.0
O C:HOH887 4.2 31.3 1.0
O C:HOH646 4.2 25.2 1.0
O C:HOH1020 4.4 30.4 1.0
O C:HOH976 4.4 33.1 1.0
O C:VAL177 4.4 13.8 1.0
O C:HOH1066 4.4 41.9 1.0
O C:HOH829 4.5 22.7 1.0
CA C:GLY180 4.7 14.7 1.0
CG1 C:VAL177 4.9 21.1 1.0

Sodium binding site 7 out of 14 in 9mva

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Sodium binding site 7 out of 14 in the Mycobacterium Abscessus EIS2 in Complex with Non-Hydrolyzable Coenzymea


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of Mycobacterium Abscessus EIS2 in Complex with Non-Hydrolyzable Coenzymea within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na509

b:28.5
occ:1.00
 O C:HOH908 2.1 23.1 1.0
O C:HOH977 2.1 21.3 1.0
O C:HOH860 2.1 25.4 1.0
O C:HOH673 2.3 26.6 1.0
O C:GLY275 2.6 24.2 1.0
O C:HOH623 2.7 19.4 1.0
O C:HOH868 2.9 34.0 1.0
C C:GLY275 3.5 21.4 1.0
CA C:GLY275 3.9 20.2 1.0
O C:HOH606 4.1 23.2 1.0
O C:HOH650 4.1 30.8 1.0
O C:HIS274 4.1 16.8 0.8
O C:ALA407 4.1 13.6 1.0
O C:HOH626 4.2 22.1 1.0
O C:GLN245 4.3 16.2 1.0
N C:ALA276 4.5 17.2 1.0
OH C:TYR273 4.7 17.1 1.0
CE1 C:TYR273 4.8 16.1 1.0
CA C:ALA276 4.9 14.3 1.0
N C:GLY275 4.9 20.4 1.0
C C:HIS274 4.9 13.8 1.0
O C:PRO408 5.0 14.9 1.0

Sodium binding site 8 out of 14 in 9mva

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Sodium binding site 8 out of 14 in the Mycobacterium Abscessus EIS2 in Complex with Non-Hydrolyzable Coenzymea


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 8 of Mycobacterium Abscessus EIS2 in Complex with Non-Hydrolyzable Coenzymea within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na508

b:20.8
occ:1.00
 O E:HOH773 2.7 18.0 1.0
OE2 D:GLU120 2.8 15.1 1.0
N E:LEU267 2.8 9.9 1.0
NH1 E:ARG269 3.0 12.1 1.0
CD D:GLU120 3.4 14.5 1.0
OE1 D:GLU120 3.5 13.3 1.0
CA E:LEU267 3.5 11.1 1.0
NH2 E:ARG143 3.6 19.3 1.0
O D:HOH703 3.7 16.3 1.0
CA E:ASP266 3.7 11.8 1.0
C E:ASP266 3.7 11.2 1.0
NH2 E:ARG269 3.7 15.1 1.0
CZ E:ARG269 3.8 13.7 1.0
O E:HOH744 3.8 15.9 1.0
CB E:ASP266 4.1 12.1 1.0
OD1 E:ASP266 4.2 15.0 1.0
O D:HOH738 4.3 13.2 1.0
C E:LEU267 4.3 14.4 1.0
N6 D:SOP502 4.6 15.6 1.0
CG E:PRO238 4.6 12.0 1.0
N E:VAL268 4.6 11.6 1.0
CZ E:ARG143 4.7 27.6 1.0
CG E:ASP266 4.7 12.4 1.0
CD2 E:LEU267 4.7 12.0 1.0
O E:VAL268 4.8 10.6 1.0
CG D:GLU120 4.8 11.8 1.0
CB E:LEU267 4.8 12.0 1.0
O E:MET265 4.9 13.6 1.0
O E:ASP266 4.9 9.5 1.0
N E:ASP266 5.0 11.1 1.0

Sodium binding site 9 out of 14 in 9mva

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Sodium binding site 9 out of 14 in the Mycobacterium Abscessus EIS2 in Complex with Non-Hydrolyzable Coenzymea


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 9 of Mycobacterium Abscessus EIS2 in Complex with Non-Hydrolyzable Coenzymea within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na509

b:25.3
occ:1.00
 O D:HOH656 2.1 20.0 1.0
O D:HOH1049 2.2 23.2 1.0
O D:HOH1061 2.2 24.8 1.0
O D:HOH991 2.2 26.3 1.0
O D:HOH901 4.1 14.3 1.0
O D:HOH640 4.2 28.1 1.0
O D:HOH910 4.2 34.6 1.0
O D:VAL177 4.3 18.0 1.0
O D:HOH1033 4.4 38.2 1.0
O D:HOH776 4.5 21.1 1.0
CA D:GLY180 4.7 17.4 1.0
CG1 D:VAL177 4.9 18.6 1.0

Sodium binding site 10 out of 14 in 9mva

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Sodium binding site 10 out of 14 in the Mycobacterium Abscessus EIS2 in Complex with Non-Hydrolyzable Coenzymea


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 10 of Mycobacterium Abscessus EIS2 in Complex with Non-Hydrolyzable Coenzymea within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na510

b:32.2
occ:1.00
 O D:HOH871 2.1 25.6 1.0
O D:HOH962 2.1 26.4 1.0
O D:HOH727 2.1 29.5 1.0
O D:HOH716 2.3 27.2 1.0
O D:HOH634 2.7 24.1 1.0
O D:GLY275 2.7 24.9 1.0
C D:GLY275 3.5 24.4 1.0
O D:ALA407 4.0 13.6 1.0
CA D:GLY275 4.0 24.2 1.0
O D:HOH622 4.1 23.2 1.0
O D:HOH633 4.1 25.8 1.0
O D:HOH623 4.1 33.2 1.0
O D:HIS274 4.3 23.6 0.8
N D:ALA276 4.5 14.4 1.0
O D:GLN245 4.5 17.6 1.0
OH D:TYR273 4.7 18.1 1.0
CA D:ALA276 4.8 14.7 1.0
O D:PRO408 4.9 14.7 1.0
CE1 D:TYR273 4.9 15.7 1.0
C D:ALA407 4.9 13.7 1.0

Reference:

T.D.Jayasinghe, A.L.Coker, T.Rajendra, D.Miller, R.E.Lee. Mycobacterium Abscessus EIS2 in Complex with Non-Hydrolyzable Coenzymea To Be Published.
Page generated: Sun Feb 9 08:43:04 2025

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