Atomistry » Sodium » PDB 4tmw-4u9k » 4tvo
Atomistry »
  Sodium »
    PDB 4tmw-4u9k »
      4tvo »

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

Go back to Sodium Binding Sites List in 4tvo
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

Go back to Sodium Binding Sites List in 4tvo
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

Go back to Sodium Binding Sites List in 4tvo
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

Go back to Sodium Binding Sites List in 4tvo
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

Go back to Sodium Binding Sites List in 4tvo
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

Go back to Sodium Binding Sites List in 4tvo
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

Go back to Sodium Binding Sites List in 4tvo
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

Go back to Sodium Binding Sites List in 4tvo
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

Go back to Sodium Binding Sites List in 4tvo
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

Go back to Sodium Binding Sites List in 4tvo
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: Mon Oct 7 18:30:28 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