Sodium in PDB 4jco: 1.7 A Resolution Structure of Wild Type Malate Dehydrogenase From Haloarcula Marismortui

All present enzymatic activity of 1.7 A Resolution Structure of Wild Type Malate Dehydrogenase From Haloarcula Marismortui:
1.1.1.37;

The structure of 1.7 A Resolution Structure of Wild Type Malate Dehydrogenase From Haloarcula Marismortui, PDB code: 4jco was solved by F.M.D.Vellieux, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	42.96 / 1.70
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	126.813, 114.065, 124.022, 90.00, 93.49, 90.00
R / Rfree (%)	22.4 / 25.7

The structure of 1.7 A Resolution Structure of Wild Type Malate Dehydrogenase From Haloarcula Marismortui also contains other interesting chemical elements:

Chlorine

(Cl)

13 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 26;

Binding sites:

The binding sites of Sodium atom in the 1.7 A Resolution Structure of Wild Type Malate Dehydrogenase From Haloarcula Marismortui (pdb code 4jco). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 26 binding sites of Sodium where determined in the 1.7 A Resolution Structure of Wild Type Malate Dehydrogenase From Haloarcula Marismortui, PDB code: 4jco:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Sodium binding site 1 out of 26 in the 1.7 A Resolution Structure of Wild Type Malate Dehydrogenase From Haloarcula Marismortui


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of 1.7 A Resolution Structure of Wild Type Malate Dehydrogenase From Haloarcula Marismortui within 5.0Å range: probe atom residue distance (Å) B Occ A:Na405 b:36.6 occ:1.00 OD2 A:ASP47 2.4 31.3 1.0 OD2 C:ASP264 2.7 26.2 1.0 O C:HOH818 2.9 37.1 1.0 CG A:ASP47 3.1 34.2 1.0 OD1 A:ASP47 3.2 41.5 1.0 O A:HOH726 3.5 37.1 1.0 CG C:ASP264 3.6 25.1 1.0 CB C:ASP264 3.6 19.8 1.0 O C:HOH670 3.6 32.5 1.0 O C:HOH713 3.6 35.5 1.0 N A:THR22 4.2 22.4 1.0 O A:HOH516 4.2 37.8 1.0 O C:HOH653 4.2 30.5 1.0 CG2 A:THR22 4.4 31.9 1.0 CB A:ASP47 4.6 24.4 1.0 O C:HOH652 4.6 30.6 1.0 OG1 A:THR22 4.7 38.0 1.0 OD1 C:ASP264 4.8 20.4 1.0 OG C:SER295 4.8 40.0 1.0 O C:ASP264 4.9 18.2 1.0 O C:HOH501 5.0 44.5 1.0

Sodium binding site 2 out of 26 in the 1.7 A Resolution Structure of Wild Type Malate Dehydrogenase From Haloarcula Marismortui


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of 1.7 A Resolution Structure of Wild Type Malate Dehydrogenase From Haloarcula Marismortui within 5.0Å range: probe atom residue distance (Å) B Occ A:Na406 b:48.0 occ:1.00 O A:HOH577 2.4 30.5 1.0 O A:SER91 2.8 26.4 1.0 OD1 A:ASN131 3.1 35.5 1.0 O A:ASP132B 3.3 54.4 1.0 N A:SER91 3.6 22.9 1.0 O A:HOH578 3.6 25.6 1.0 C A:GLY90 3.7 27.5 1.0 CB A:ASN131 3.8 26.7 1.0 CA A:GLY90 3.8 27.5 1.0 C A:SER91 3.8 21.1 1.0 CG A:ASN131 3.8 30.1 1.0 C A:ASP132B 4.0 49.9 1.0 N A:GLY90 4.0 29.5 1.0 CA A:ASN131 4.1 30.4 1.0 N A:ASP132A 4.1 53.5 1.0 CB A:TYR133 4.2 27.0 1.0 CA A:SER91 4.3 19.4 1.0 N A:ASP132B 4.4 60.9 1.0 O A:GLY90 4.4 27.0 1.0 C A:ASN131 4.5 40.4 1.0 N A:TYR133 4.6 26.2 1.0 CA A:TYR133 4.6 21.5 1.0 OD1 A:ASP132B 4.8 73.9 1.0 CA A:ASP132B 4.9 57.2 1.0 CD1 A:TYR133 4.9 26.6 1.0 CB A:SER91 4.9 23.2 1.0 N A:ASP92 4.9 19.0 1.0

Sodium binding site 3 out of 26 in the 1.7 A Resolution Structure of Wild Type Malate Dehydrogenase From Haloarcula Marismortui


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of 1.7 A Resolution Structure of Wild Type Malate Dehydrogenase From Haloarcula Marismortui within 5.0Å range: probe atom residue distance (Å) B Occ A:Na407 b:35.4 occ:1.00 O A:HOH594 2.4 31.0 1.0 O A:HOH592 2.6 33.0 1.0 O A:TYR150 3.0 25.0 1.0 O A:HOH595 3.2 28.6 1.0 O A:HOH751 3.3 38.5 1.0 O A:GLY153 3.3 24.8 1.0 O A:GLU151 3.6 29.6 1.0 CZ A:TYR150 3.6 26.8 1.0 CE1 A:TYR150 3.7 26.1 1.0 O A:HOH804 3.8 37.9 1.0 CA A:GLU151 3.9 24.0 1.0 C A:TYR150 3.9 25.9 1.0 OH A:TYR150 3.9 24.7 1.0 C A:GLU151 4.0 29.6 1.0 CE2 A:TYR150 4.0 26.3 1.0 CD1 A:TYR150 4.1 26.1 1.0 O A:HOH797 4.2 28.5 1.0 O A:HOH803 4.2 42.1 1.0 N A:GLU151 4.3 25.7 1.0 CD2 A:TYR150 4.4 22.4 1.0 C A:GLY153 4.4 30.5 1.0 CG A:TYR150 4.5 23.4 1.0 OE1 A:GLU151 4.6 24.2 1.0 O A:ARG155 4.8 27.3 1.0 O A:HOH802 4.9 42.5 1.0 N A:GLY153 4.9 23.4 1.0

Sodium binding site 4 out of 26 in the 1.7 A Resolution Structure of Wild Type Malate Dehydrogenase From Haloarcula Marismortui


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of 1.7 A Resolution Structure of Wild Type Malate Dehydrogenase From Haloarcula Marismortui within 5.0Å range: probe atom residue distance (Å) B Occ A:Na408 b:27.0 occ:1.00 O B:HOH556 2.4 36.6 1.0 OE2 B:GLU247 2.7 23.2 1.0 OE2 A:GLU247 2.7 24.7 1.0 O B:HOH773 2.9 48.2 1.0 O B:HOH635 3.5 29.1 1.0 O A:HOH657 3.5 17.9 1.0 CD B:GLU247 3.6 25.6 1.0 O B:HOH637 3.6 19.2 1.0 O B:HOH636 3.6 17.5 1.0 CD A:GLU247 3.6 26.7 1.0 OE1 B:GLU247 3.7 23.9 1.0 OE1 A:GLU247 3.7 22.9 1.0 O B:HOH501 3.7 35.1 1.0 O A:HOH659 3.8 20.5 1.0 O A:HOH658 3.8 21.9 1.0 O B:HOH772 4.6 30.2 1.0 O B:HOH502 4.6 52.0 1.0 CH2 B:TRP248 4.9 21.5 1.0 CH2 A:TRP248 4.9 21.2 1.0 CG B:GLU247 5.0 21.6 1.0

Sodium binding site 5 out of 26 in the 1.7 A Resolution Structure of Wild Type Malate Dehydrogenase From Haloarcula Marismortui


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of 1.7 A Resolution Structure of Wild Type Malate Dehydrogenase From Haloarcula Marismortui within 5.0Å range: probe atom residue distance (Å) B Occ A:Na409 b:36.7 occ:1.00 OD1 C:ASP47 2.4 42.1 1.0 O A:ASP264 2.4 17.2 1.0 O C:HOH517 2.5 32.5 1.0 O A:HOH715 3.0 52.7 1.0 OD2 A:ASP264 3.1 24.6 1.0 CG C:ASP47 3.4 32.9 1.0 CG A:ASP264 3.5 24.1 1.0 O C:HOH514 3.6 32.4 1.0 C A:ASP264 3.6 19.3 1.0 CB A:ASP264 3.7 21.9 1.0 O A:HOH665 3.7 21.5 1.0 O C:HOH711 3.8 29.4 1.0 OD2 C:ASP47 4.1 30.6 1.0 O A:HOH663 4.2 31.2 1.0 O A:HOH661 4.2 48.4 1.0 O A:HIS263 4.2 18.3 1.0 CA A:ASP264 4.3 18.2 1.0 OD1 A:ASP264 4.4 21.4 1.0 CB C:ASP47 4.4 25.6 1.0 O A:HOH664 4.5 41.4 1.0 O C:HOH537 4.6 23.7 1.0 O C:HOH710 4.6 31.3 1.0 N A:THR265 4.6 16.6 1.0 O C:HOH518 4.7 43.3 1.0 CA A:THR265 4.8 15.1 1.0 O C:HOH729 4.9 29.5 1.0 CA C:ASP47 4.9 25.1 1.0

Sodium binding site 6 out of 26 in the 1.7 A Resolution Structure of Wild Type Malate Dehydrogenase From Haloarcula Marismortui


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of 1.7 A Resolution Structure of Wild Type Malate Dehydrogenase From Haloarcula Marismortui within 5.0Å range: probe atom residue distance (Å) B Occ A:Na410 b:36.0 occ:1.00 O B:HOH591 2.4 31.5 1.0 O A:HOH530 2.5 24.2 1.0 OD1 A:ASN67 2.8 18.8 1.0 O A:THR76 3.2 17.9 1.0 CG A:ASN67 3.7 19.8 1.0 CD1 B:TYR174 3.7 18.3 1.0 CE1 B:TYR174 3.9 18.4 1.0 CB A:ASN67 4.0 16.7 1.0 CA A:ARG77 4.0 20.9 1.0 C A:THR76 4.2 14.8 1.0 CA A:ASN67 4.3 19.0 1.0 O B:HOH506 4.4 19.0 1.0 CG1 B:VAL184 4.4 16.8 1.0 O A:ASN67 4.5 16.0 1.0 N A:ARG77 4.6 16.8 1.0 CD1 A:ILE70 4.6 19.7 1.0 N A:VAL78 4.6 17.8 1.0 CG1 A:ILE70 4.6 19.7 1.0 O B:HOH855 4.7 35.5 1.0 CG A:ARG77 4.7 33.6 1.0 ND2 A:ASN67 4.7 19.5 1.0 CB B:VAL184 4.7 15.3 1.0 CB A:ARG77 4.8 22.1 1.0 O B:HOH592 4.8 36.9 1.0 CG B:TYR174 4.8 19.6 1.0 C A:ASN67 4.8 21.0 1.0 C A:ARG77 4.9 22.9 1.0

Sodium binding site 7 out of 26 in the 1.7 A Resolution Structure of Wild Type Malate Dehydrogenase From Haloarcula Marismortui


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of 1.7 A Resolution Structure of Wild Type Malate Dehydrogenase From Haloarcula Marismortui within 5.0Å range: probe atom residue distance (Å) B Occ B:Na403 b:39.1 occ:1.00 O B:THR76 2.5 19.8 1.0 O B:HOH701 2.5 30.8 1.0 O B:SER74 2.8 23.2 1.0 O A:HOH754 3.0 29.6 1.0 CG1 A:VAL184 3.2 17.7 1.0 O B:HOH534 3.3 21.4 1.0 C B:ASN75 3.3 18.4 1.0 C B:THR76 3.5 15.5 1.0 N B:THR76 3.6 19.8 1.0 O B:ASN75 3.6 20.9 1.0 O B:HOH511 3.6 24.8 1.0 CA B:ASN75 3.7 18.4 1.0 CD1 B:ILE70 3.7 17.6 1.0 C B:SER74 3.7 14.6 1.0 CG1 B:ILE70 3.8 17.4 1.0 N B:ASN75 4.1 14.5 1.0 CB A:VAL184 4.1 15.5 1.0 CA B:THR76 4.1 14.5 1.0 N B:ARG77 4.5 17.3 1.0 CA B:ARG77 4.8 20.6 1.0 OD1 B:ASN67 4.8 21.4 1.0 CA B:SER74 5.0 13.8 1.0 OG B:SER74 5.0 18.0 1.0 CB B:THR76 5.0 15.2 1.0 O B:ILE70 5.0 16.9 1.0

Sodium binding site 8 out of 26 in the 1.7 A Resolution Structure of Wild Type Malate Dehydrogenase From Haloarcula Marismortui


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 8 of 1.7 A Resolution Structure of Wild Type Malate Dehydrogenase From Haloarcula Marismortui within 5.0Å range: probe atom residue distance (Å) B Occ B:Na404 b:41.1 occ:1.00 O B:HOH832 2.3 49.5 1.0 O B:ASP132B 2.5 54.4 1.0 O B:HOH785 2.7 46.7 1.0 O B:SER91 2.7 26.4 1.0 O B:HOH783 2.8 39.9 1.0 C B:ASP132B 3.7 52.1 1.0 C B:SER91 3.7 23.0 1.0 O B:HOH551 4.0 20.4 1.0 CA B:TYR133 4.2 21.7 1.0 CA B:ASP92 4.2 20.6 1.0 CB B:TYR133 4.3 27.7 1.0 N B:ASP92 4.4 19.0 1.0 N B:TYR133 4.4 28.5 1.0 C B:GLY90 4.5 30.0 1.0 O B:GLY90 4.5 30.7 1.0 N B:SER91 4.6 25.9 1.0 OD2 B:ASP92 4.6 31.7 1.0 N B:ASP132B 4.8 60.8 1.0 OD2 B:ASP132B 4.8 76.8 1.0 CA B:SER91 4.8 16.7 1.0 CA B:ASP132B 4.8 57.8 1.0 CG B:ASP132B 4.9 72.3 1.0 OD1 B:ASP132B 4.9 72.7 1.0 CA B:GLY90 4.9 29.8 1.0 C B:ASP92 5.0 19.8 1.0 O B:ASP92 5.0 22.6 1.0

Sodium binding site 9 out of 26 in the 1.7 A Resolution Structure of Wild Type Malate Dehydrogenase From Haloarcula Marismortui


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 9 of 1.7 A Resolution Structure of Wild Type Malate Dehydrogenase From Haloarcula Marismortui within 5.0Å range: probe atom residue distance (Å) B Occ B:Na405 b:40.9 occ:1.00 O B:HOH724 2.4 34.5 1.0 O B:HOH805 2.5 38.1 1.0 O B:HOH604 2.8 32.4 1.0 O B:HOH858 2.9 52.4 1.0 O B:GLY196 3.1 20.6 1.0 O B:HOH725 3.4 44.9 1.0 C B:GLY196 3.5 18.1 1.0 CA B:GLY196 3.6 21.9 1.0 O B:HOH627 3.6 27.1 1.0 N B:GLY196 3.6 25.1 1.0 OE1 B:GLN199 3.6 32.8 1.0 CD B:GLN199 4.2 36.5 1.0 O B:HOH588 4.3 24.5 1.0 N B:ASP197 4.5 22.3 1.0 C B:HIS195 4.6 22.3 1.0 OD1 B:ASP168 4.7 24.7 1.0 CG B:GLN199 4.8 33.7 1.0 NE2 B:GLN199 5.0 36.8 1.0

Sodium binding site 10 out of 26 in the 1.7 A Resolution Structure of Wild Type Malate Dehydrogenase From Haloarcula Marismortui


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 10 of 1.7 A Resolution Structure of Wild Type Malate Dehydrogenase From Haloarcula Marismortui within 5.0Å range: probe atom residue distance (Å) B Occ B:Na406 b:41.3 occ:1.00 OD1 D:ASP47 2.3 41.5 1.0 O D:HOH787 2.4 37.6 1.0 O B:ASP264 2.4 17.1 1.0 OD2 B:ASP264 2.7 27.9 1.0 O B:HOH642 2.8 50.1 1.0 CG B:ASP264 3.1 25.1 1.0 CG D:ASP47 3.2 34.7 1.0 O D:HOH526 3.3 29.2 1.0 CB B:ASP264 3.3 20.5 1.0 C B:ASP264 3.5 20.8 1.0 OD2 D:ASP47 3.7 30.9 1.0 O D:HOH517 3.8 43.8 1.0 O B:HOH643 3.9 29.5 1.0 CA B:ASP264 4.0 20.6 1.0 OD1 B:ASP264 4.1 23.2 1.0 O D:HOH830 4.2 47.6 1.0 O B:HIS263 4.2 20.3 1.0 CB D:ASP47 4.4 26.8 1.0 O D:HOH520 4.6 31.6 1.0 N B:THR265 4.7 18.7 1.0 N B:ASP264 5.0 19.9 1.0

F.M.D.Vellieux, F.M.D.Vellieux. N/A N/A.