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Sodium in PDB 4tvo: Structure of Malate Dehydrogenase From Mycobacterium Tuberculosis

Enzymatic activity of Structure of Malate Dehydrogenase From Mycobacterium Tuberculosis

All present enzymatic activity of Structure of Malate Dehydrogenase From Mycobacterium Tuberculosis:
1.1.1.37;

Protein crystallography data

The structure of Structure of Malate Dehydrogenase From Mycobacterium Tuberculosis, PDB code: 4tvo was solved by D.M.Ferraris, M.Rizzi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 77.76 / 1.50
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 52.606, 79.307, 155.513, 90.00, 90.00, 90.00
R / Rfree (%) 16.6 / 19.3

Sodium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 22;

Binding sites:

The binding sites of Sodium atom in the Structure of Malate Dehydrogenase From Mycobacterium Tuberculosis (pdb code 4tvo). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 22 binding sites of Sodium where determined in the Structure of Malate Dehydrogenase From Mycobacterium Tuberculosis, PDB code: 4tvo:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Sodium binding site 1 out of 22 in 4tvo

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Sodium binding site 1 out of 22 in the Structure of Malate Dehydrogenase From Mycobacterium Tuberculosis


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure of Malate Dehydrogenase From Mycobacterium Tuberculosis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na402

b:23.4
occ:1.00
 O A:ARG36 2.7 19.4 1.0
O A:HOH569 2.7 14.6 1.0
O A:GLY33 2.8 19.3 1.0
N A:GLY33 3.4 14.1 1.0
N A:LEU32 3.5 14.9 1.0
CB A:LEU32 3.5 16.9 1.0
C A:LEU32 3.6 18.3 1.0
CA A:GLY29 3.6 14.6 1.0
CA A:LEU32 3.7 15.3 1.0
C A:GLY33 3.8 20.7 1.0
C A:ARG36 3.8 18.8 1.0
CB A:ARG36 3.9 21.1 1.0
O A:GLY29 3.9 16.2 1.0
CD1 A:LEU66 3.9 17.5 1.0
C A:GLY29 4.0 15.1 1.0
CG1 A:ILE38 4.1 21.1 1.0
CD1 A:ILE38 4.1 19.9 1.0
CA A:GLY33 4.1 18.1 1.0
CA A:ARG36 4.2 19.1 1.0
O A:LEU32 4.3 19.9 1.0
N A:ARG36 4.3 19.5 1.0
CG A:LEU32 4.4 21.5 1.0
N A:GLY29 4.6 13.2 1.0
C A:LEU31 4.7 15.8 1.0
CD1 A:LEU32 4.8 26.5 1.0
O A:LEU26 4.8 13.7 1.0
N A:LEU31 4.8 13.4 1.0
CG A:LEU66 4.9 16.1 1.0
N A:PRO37 5.0 15.9 1.0
N A:SER30 5.0 13.8 1.0

Sodium binding site 2 out of 22 in 4tvo

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Sodium binding site 2 out of 22 in the Structure of Malate Dehydrogenase From Mycobacterium Tuberculosis


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Structure of Malate Dehydrogenase From Mycobacterium Tuberculosis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na403

b:22.6
occ:1.00
 O B:ASP61 2.9 13.9 1.0
ND2 A:ASN163 3.0 11.8 1.0
O A:SER243 3.1 11.1 1.0
CB A:ALA247 3.4 9.7 1.0
CA B:CYS62 3.4 12.3 1.0
CD1 A:LEU160 3.4 15.4 1.0
O A:HOH581 3.5 17.7 1.0
N A:ALA247 3.6 10.2 1.0
CB A:ASN163 3.7 10.3 1.0
CA A:ALA247 3.7 9.9 1.0
C B:ASP61 3.8 13.1 1.0
CG A:ASN163 3.8 11.5 1.0
N B:CYS62 4.0 12.0 1.0
C A:SER243 4.1 10.4 1.0
C B:CYS62 4.2 14.1 1.0
O B:CYS62 4.3 14.6 1.0
CB B:CYS62 4.3 13.1 1.0
C A:SER246 4.3 11.0 1.0
SG B:CYS62 4.3 13.5 1.0
CA A:LEU160 4.3 10.0 1.0
CB A:SER246 4.4 12.0 1.0
CA A:SER243 4.5 9.8 1.0
CB A:SER243 4.5 10.9 1.0
CG A:LEU160 4.6 15.1 1.0
CB A:LEU160 4.7 11.8 1.0
OD2 A:ASP250 4.7 17.2 1.0
OG A:SER246 4.8 13.9 1.0
O A:ARG159 4.8 11.8 1.0
CA A:SER246 4.9 10.2 1.0
O A:LEU160 5.0 10.4 1.0
O A:SER246 5.0 11.1 1.0

Sodium binding site 3 out of 22 in 4tvo

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Sodium binding site 3 out of 22 in the Structure of Malate Dehydrogenase From Mycobacterium Tuberculosis


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Structure of Malate Dehydrogenase From Mycobacterium Tuberculosis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na404

b:25.1
occ:1.00
 O A:HOH640 2.7 30.3 1.0
O A:ILE149 2.8 15.4 1.0
O A:MET143 2.8 14.7 1.0
O A:ALA146 3.0 16.8 1.0
CG A:MET143 3.5 16.2 1.0
CG A:ARG151 3.5 23.1 1.0
CA A:ARG151 3.7 14.1 1.0
C A:MET143 3.7 13.2 1.0
N A:ARG151 3.8 14.8 1.0
C A:ALA146 3.8 16.0 1.0
CE1 A:PHE154 3.8 14.8 1.0
C A:ILE149 4.0 14.3 1.0
C A:PRO150 4.0 14.5 1.0
CA A:MET143 4.1 11.8 1.0
CB A:ARG151 4.2 17.0 1.0
CD1 A:PHE154 4.2 14.9 1.0
O A:PRO150 4.3 14.8 1.0
CB A:MET143 4.4 14.1 1.0
CA A:PRO147 4.5 22.4 1.0
O A:HOH741 4.5 48.7 1.0
N A:PRO147 4.6 18.6 1.0
CB A:ALA146 4.6 17.4 1.0
CA A:ALA146 4.6 15.9 1.0
O A:HOH692 4.7 38.7 1.0
CZ A:PHE154 4.7 13.7 1.0
CD A:ARG151 4.7 30.2 1.0
N A:THR144 4.8 13.4 1.0
CA A:ILE149 4.8 15.9 1.0
CA A:PRO150 4.8 16.5 1.0
CB A:ILE149 4.9 15.2 1.0
C A:ARG151 4.9 13.1 1.0
N A:ILE149 4.9 16.7 1.0
SD A:MET143 4.9 15.8 1.0
N A:ALA146 4.9 15.7 1.0
C A:PRO147 4.9 20.3 1.0
NH1 A:ARG151 4.9 40.8 1.0
N A:PRO150 4.9 14.5 1.0
O A:PRO147 5.0 23.9 1.0

Sodium binding site 4 out of 22 in 4tvo

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Sodium binding site 4 out of 22 in the Structure of Malate Dehydrogenase From Mycobacterium Tuberculosis


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Structure of Malate Dehydrogenase From Mycobacterium Tuberculosis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na405

b:26.9
occ:1.00
 OD1 A:ASP319 2.7 30.5 1.0
O A:ALA315 2.8 13.3 1.0
CG A:ASP319 3.2 26.4 1.0
OD2 A:ASP319 3.4 33.4 1.0
C A:ALA315 3.5 12.8 1.0
CB A:ALA315 3.7 15.4 1.0
CA A:ALA315 3.7 13.0 1.0
N A:ASP319 4.2 12.6 1.0
CB A:ASP319 4.3 16.1 1.0
CB A:ALA318 4.4 12.3 1.0
CA A:ASP319 4.6 15.1 1.0
N A:GLU316 4.6 12.5 1.0
C A:ALA318 4.9 12.8 1.0

Sodium binding site 5 out of 22 in 4tvo

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Sodium binding site 5 out of 22 in the Structure of Malate Dehydrogenase From Mycobacterium Tuberculosis


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Structure of Malate Dehydrogenase From Mycobacterium Tuberculosis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na406

b:24.7
occ:1.00
 O A:HOH672 2.7 32.6 1.0
O A:THR224 2.7 16.6 1.0
NA A:NA407 2.8 27.9 1.0
CA A:ARG228 3.3 14.5 1.0
N A:ARG228 3.5 14.9 1.0
C A:THR224 3.6 14.5 1.0
CB A:ALA231 3.6 23.4 1.0
C A:LYS227 3.6 18.8 1.0
O A:LYS227 3.6 18.4 1.0
CA A:THR224 3.7 15.2 1.0
CG2 A:THR224 3.9 18.5 1.0
CD A:ARG228 3.9 14.3 1.0
O A:HOH698 3.9 41.6 1.0
CB A:ARG228 4.0 13.3 1.0
CB A:THR224 4.3 17.4 1.0
O A:PRO223 4.4 17.4 1.0
CB A:LYS227 4.4 21.1 1.0
C A:ARG228 4.4 15.6 1.0
CA A:LYS227 4.5 19.3 1.0
CG A:ARG228 4.5 14.1 1.0
O A:ARG228 4.7 16.5 1.0
O A:HOH743 4.7 36.6 1.0
N A:LYS227 4.8 17.3 1.0
O A:HOH742 4.8 42.3 1.0
N A:THR224 4.9 17.0 1.0
OG1 A:THR224 4.9 18.9 1.0
N A:VAL225 4.9 14.1 1.0
CA A:ALA231 4.9 19.8 1.0
NH1 A:ARG228 4.9 17.3 1.0
N A:ALA231 5.0 21.2 1.0

Sodium binding site 6 out of 22 in 4tvo

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Sodium binding site 6 out of 22 in the Structure of Malate Dehydrogenase From Mycobacterium Tuberculosis


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Structure of Malate Dehydrogenase From Mycobacterium Tuberculosis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na407

b:27.9
occ:1.00
 O A:HOH743 2.7 36.6 1.0
O A:HOH742 2.8 42.3 1.0
NA A:NA406 2.8 24.7 1.0
NH1 A:ARG228 2.9 17.3 1.0
CD A:ARG228 3.6 14.3 1.0
CB A:ALA231 3.7 23.4 1.0
CZ A:ARG228 3.9 16.6 1.0
CG2 A:THR224 4.0 18.5 1.0
CE B:MET57 4.1 23.8 1.0
NE A:ARG228 4.1 15.5 1.0
O A:HOH664 4.2 36.8 1.0
O A:HOH672 4.3 32.6 1.0
O A:THR224 4.7 16.6 1.0
CG A:ARG228 5.0 14.1 1.0

Sodium binding site 7 out of 22 in 4tvo

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Sodium binding site 7 out of 22 in the Structure of Malate Dehydrogenase From Mycobacterium Tuberculosis


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of Structure of Malate Dehydrogenase From Mycobacterium Tuberculosis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na408

b:27.9
occ:1.00
 O A:HOH638 2.7 27.9 1.0
O A:GLN17 2.7 12.2 1.0
OG A:SER21 2.8 31.6 1.0
O A:HOH693 2.9 33.8 1.0
CE2 B:TYR20 3.6 13.2 1.0
C A:GLN17 3.7 12.5 1.0
N A:SER21 3.8 13.6 1.0
CB A:TYR20 3.9 12.6 1.0
CB A:SER21 4.0 18.4 1.0
CD2 B:TYR20 4.0 13.5 1.0
CA A:GLN17 4.1 14.2 1.0
CB A:ALA241 4.1 13.1 1.0
CD2 A:TYR20 4.2 13.4 1.0
C A:TYR20 4.3 12.6 1.0
CB A:GLN17 4.3 18.1 1.0
CA A:SER21 4.3 15.5 1.0
O B:HOH557 4.5 20.2 1.0
CA A:TYR20 4.5 12.0 1.0
CG A:TYR20 4.5 12.3 1.0
CZ B:TYR20 4.8 13.0 1.0
O B:HOH558 4.8 19.8 1.0
O A:TYR20 4.9 15.0 1.0
N A:ILE18 4.9 12.6 1.0
N A:TYR20 4.9 11.9 1.0
O A:HOH579 4.9 18.2 1.0
N A:ALA242 4.9 11.0 1.0

Sodium binding site 8 out of 22 in 4tvo

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Sodium binding site 8 out of 22 in the Structure of Malate Dehydrogenase From Mycobacterium Tuberculosis


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 8 of Structure of Malate Dehydrogenase From Mycobacterium Tuberculosis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na409

b:31.6
occ:1.00
 O A:HOH669 2.8 39.3 1.0
N A:ILE72 3.0 13.7 1.0
OE1 A:GLU71 3.5 45.8 1.0
CA A:GLU71 3.5 18.2 1.0
O A:ILE72 3.6 15.8 1.0
C A:GLU71 3.7 16.6 1.0
CG1 A:ILE72 3.8 19.6 1.0
CA A:ILE72 3.9 14.5 1.0
O A:VAL70 4.2 20.5 1.0
C A:ILE72 4.2 16.4 1.0
CB A:ILE72 4.3 18.7 1.0
CB A:GLU71 4.3 22.4 1.0
CD A:GLU71 4.4 41.3 1.0
CG2 A:ILE72 4.6 17.4 1.0
N A:GLU71 4.7 15.9 1.0
C A:VAL70 4.8 18.9 1.0
O A:GLU71 4.9 17.0 1.0
CD1 A:ILE72 4.9 23.4 1.0
CG A:GLU71 5.0 35.8 1.0

Sodium binding site 9 out of 22 in 4tvo

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Sodium binding site 9 out of 22 in the Structure of Malate Dehydrogenase From Mycobacterium Tuberculosis


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 9 of Structure of Malate Dehydrogenase From Mycobacterium Tuberculosis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na410

b:31.6
occ:1.00
 O A:GLU218 2.6 18.6 1.0
NH1 A:ARG309 2.9 22.0 1.0
NH2 A:ARG309 3.1 25.3 1.0
CZ A:ARG309 3.4 23.0 1.0
C A:GLU218 3.7 17.9 1.0
CG2 A:ILE222 3.9 16.3 1.0
CB A:ILE222 3.9 15.5 1.0
CD A:PRO223 3.9 15.3 1.0
O A:HOH536 3.9 35.6 1.0
CA A:GLU218 4.1 17.6 1.0
O A:HOH696 4.3 31.9 1.0
CG A:PRO223 4.4 18.8 1.0
CD1 A:ILE222 4.4 18.1 1.0
CB A:GLU218 4.5 20.8 1.0
CG1 A:ILE222 4.7 15.2 1.0
O A:HOH505 4.7 34.7 1.0
N A:PRO223 4.8 14.8 1.0
NE A:ARG309 4.8 21.8 1.0
N A:ASP219 4.9 16.4 1.0

Sodium binding site 10 out of 22 in 4tvo

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Sodium binding site 10 out of 22 in the Structure of Malate Dehydrogenase From Mycobacterium Tuberculosis


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 10 of Structure of Malate Dehydrogenase From Mycobacterium Tuberculosis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na411

b:33.3
occ:1.00
 OD2 B:ASP60 2.6 22.5 1.0
NH2 A:ARG228 2.8 16.8 1.0
O A:HOH664 3.2 36.8 1.0
CG B:ASP60 3.5 23.7 1.0
CB B:ASP60 3.6 16.7 1.0
CZ A:ARG228 3.8 16.6 1.0
NH1 A:ARG228 3.9 17.3 1.0
CA B:MET57 4.0 13.9 1.0
CG B:MET57 4.2 17.4 1.0
O B:HOH681 4.3 39.4 1.0
CB B:MET57 4.4 15.1 1.0
O B:MET57 4.5 14.1 1.0
O B:VAL56 4.7 13.9 1.0
OD1 B:ASP60 4.7 23.3 1.0
C B:MET57 4.7 13.0 1.0
NE2 A:GLN168 4.8 22.7 1.0
N B:MET57 4.8 14.9 1.0
O B:HOH623 5.0 29.9 1.0
OD1 B:ASP61 5.0 16.4 1.0

Reference:

D.M.Ferraris, R.Spallek, W.Oehlmann, M.Singh, M.Rizzi. Structures of Citrate Synthase and Malate Dehydrogenase of Mycobacterium Tuberculosis. Proteins V. 83 389 2015.
ISSN: ESSN 1097-0134
PubMed: 25524525
DOI: 10.1002/PROT.24743
Page generated: Tue Dec 15 07:38:09 2020

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