Sodium in PDB 6nzy: Structural Determination of the Carboxy-Terminal Portion of Atp- Citrate Lyase

The structure of Structural Determination of the Carboxy-Terminal Portion of Atp- Citrate Lyase, PDB code: 6nzy was solved by V.H.Nguyen, M.E.Fraser, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	71.17 / 1.90
Space group	P 32
Cell size a, b, c (Å), α, β, γ (°)	82.180, 82.180, 151.200, 90.00, 90.00, 120.00
R / Rfree (%)	16.7 / 19

The binding sites of Sodium atom in the Structural Determination of the Carboxy-Terminal Portion of Atp- Citrate Lyase (pdb code 6nzy). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 8 binding sites of Sodium where determined in the Structural Determination of the Carboxy-Terminal Portion of Atp- Citrate Lyase, PDB code: 6nzy:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Sodium binding site 1 out of 8 in the Structural Determination of the Carboxy-Terminal Portion of Atp- Citrate Lyase


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structural Determination of the Carboxy-Terminal Portion of Atp- Citrate Lyase within 5.0Å range: probe atom residue distance (Å) B Occ A:Na711 b:57.0 occ:1.00 OD1 A:ASP434 2.2 30.9 0.6 O C:HOH807 2.4 46.6 1.0 HD22 C:ASN561 2.5 57.9 1.0 H A:MET435 2.8 30.0 1.0 HB3 A:MET435 2.9 33.5 1.0 CG A:ASP434 3.1 32.8 0.6 HD3 A:PRO436 3.2 31.1 1.0 OD2 A:ASP434 3.3 35.1 0.6 HB2 A:MET435 3.3 33.5 1.0 ND2 C:ASN561 3.4 48.2 1.0 HB3 C:ASN561 3.4 49.2 1.0 CB A:MET435 3.5 27.9 1.0 HB2 C:ASN561 3.5 49.2 1.0 HB3 A:ASP434 3.6 37.4 0.5 N A:MET435 3.6 25.0 1.0 HH2 A:TRP576 3.8 37.1 1.0 HE3 A:MET435 3.8 34.8 1.0 CB C:ASN561 3.8 41.0 1.0 HD21 C:ASN561 3.9 57.9 1.0 CH2 A:TRP576 4.0 30.9 1.0 CD A:PRO436 4.1 25.9 1.0 CG C:ASN561 4.1 46.1 1.0 CA A:MET435 4.2 26.4 1.0 HD2 A:PRO436 4.3 31.1 1.0 O C:HOH847 4.4 44.5 1.0 CZ2 A:TRP576 4.4 27.6 1.0 HZ2 A:TRP576 4.4 33.1 1.0 CB A:ASP434 4.4 31.2 1.0 HA A:ASP434 4.5 33.9 1.0 CZ3 A:TRP576 4.6 29.1 1.0 CE A:MET435 4.6 29.0 1.0 O C:HIS558 4.7 47.2 1.0 C A:ASP434 4.7 27.7 1.0 HZ3 A:TRP576 4.7 34.9 1.0 CG A:MET435 4.7 28.4 1.0 CA A:ASP434 4.8 28.2 1.0 HB3 A:ASP434 4.8 37.4 0.6 HG3 A:PRO436 4.9 33.1 1.0 SD A:MET435 4.9 32.0 1.0 HA A:MET435 4.9 31.6 1.0 CG A:PRO436 5.0 27.6 1.0 CG A:ASP434 5.0 33.2 0.5 HG1 C:THR455 5.0 70.1 1.0 N A:PRO436 5.0 25.6 1.0

Sodium binding site 2 out of 8 in the Structural Determination of the Carboxy-Terminal Portion of Atp- Citrate Lyase


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Structural Determination of the Carboxy-Terminal Portion of Atp- Citrate Lyase within 5.0Å range: probe atom residue distance (Å) B Occ A:Na712 b:48.8 occ:1.00 OD1 A:ASP362 2.1 46.8 1.0 H A:ASP362 2.2 31.7 1.0 OH D:TYR596 2.6 36.5 1.0 HD2 C:PRO417 2.7 35.8 1.0 HE1 D:TYR596 2.7 45.7 1.0 HA3 C:GLY416 2.7 35.8 1.0 O C:HOH832 2.8 37.3 1.0 CG A:ASP362 3.0 40.1 1.0 N A:ASP362 3.0 26.4 1.0 HH D:TYR596 3.2 43.8 1.0 CE1 D:TYR596 3.3 38.0 1.0 HH22 D:ARG588 3.3 46.2 0.6 HA A:ASP361 3.3 40.5 1.0 CZ D:TYR596 3.4 37.7 1.0 HB3 A:ASP362 3.5 33.5 1.0 HH21 D:ARG588 3.6 45.8 0.4 CB A:ASP362 3.6 27.9 1.0 CD C:PRO417 3.6 29.8 1.0 CA C:GLY416 3.6 29.9 1.0 HH22 D:ARG588 3.6 45.8 0.4 HG3 A:ARG363 3.7 42.2 1.0 CA A:ASP362 3.8 25.6 1.0 HA2 C:GLY416 3.8 35.8 1.0 OD2 A:ASP362 3.9 40.8 1.0 NH2 D:ARG588 3.9 38.5 0.6 NH2 D:ARG588 3.9 38.1 0.4 HH21 D:ARG588 4.0 46.2 0.6 HD3 C:PRO417 4.0 35.8 1.0 C A:ASP361 4.0 31.6 1.0 H C:ALA418 4.0 35.1 1.0 CA A:ASP361 4.1 33.8 1.0 O C:HIS415 4.1 31.8 1.0 OD1 A:ASP361 4.1 32.2 1.0 H A:ARG363 4.1 35.2 1.0 N C:PRO417 4.2 29.9 1.0 C A:ASP362 4.3 30.4 1.0 C C:GLY416 4.3 28.6 1.0 N A:ARG363 4.4 29.3 1.0 HB3 C:ALA418 4.4 36.0 1.0 HG2 C:PRO417 4.4 33.7 1.0 HB2 C:ALA418 4.4 36.0 1.0 HB2 A:ASP362 4.5 33.5 1.0 CD1 D:TYR596 4.6 38.4 1.0 N C:GLY416 4.6 30.5 1.0 OD1 D:ASP591 4.6 38.1 1.0 CG C:PRO417 4.6 28.1 1.0 HA A:ASP362 4.6 30.7 1.0 CG A:ARG363 4.7 35.2 1.0 CE2 D:TYR596 4.7 36.8 1.0 C C:HIS415 4.7 29.3 1.0 N C:ALA418 4.8 29.3 1.0 HG2 A:ARG363 4.9 42.2 1.0 HD1 D:TYR596 4.9 46.1 1.0 CB C:ALA418 4.9 30.0 1.0 HH12 D:ARG588 4.9 46.6 0.6 N A:ASP361 4.9 30.1 1.0 CZ D:ARG588 5.0 39.1 0.6

Sodium binding site 3 out of 8 in the Structural Determination of the Carboxy-Terminal Portion of Atp- Citrate Lyase


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Structural Determination of the Carboxy-Terminal Portion of Atp- Citrate Lyase within 5.0Å range: probe atom residue distance (Å) B Occ A:Na713 b:59.5 occ:1.00 OD1 D:ASP362 2.2 53.1 1.0 O B:HOH848 2.4 40.4 1.0 H D:ASP362 2.6 40.0 1.0 HD2 B:PRO417 2.7 31.8 1.0 OH A:TYR596 2.7 36.4 1.0 HA3 B:GLY416 2.7 31.5 1.0 HE1 A:TYR596 2.8 37.1 1.0 HH21 A:ARG588 2.9 42.9 0.4 CG D:ASP362 3.1 42.4 1.0 HH22 A:ARG588 3.2 42.9 0.4 HH A:TYR596 3.3 43.7 1.0 HH22 A:ARG588 3.3 45.9 0.6 NH2 A:ARG588 3.3 35.7 0.4 N D:ASP362 3.4 33.4 1.0 CE1 A:TYR596 3.4 30.9 1.0 CZ A:TYR596 3.5 34.3 1.0 CD B:PRO417 3.6 26.5 1.0 HA D:ASP361 3.6 40.1 1.0 H B:ALA418 3.7 30.4 1.0 CA B:GLY416 3.7 26.3 1.0 HB3 D:ASP362 3.7 43.3 1.0 CB D:ASP362 3.8 36.1 1.0 OD2 D:ASP362 3.9 42.9 1.0 NH2 A:ARG588 3.9 38.3 0.6 HG3 D:ARG363 3.9 46.1 1.0 HB3 B:ALA418 3.9 33.7 1.0 HA2 B:GLY416 4.0 31.5 1.0 O B:HIS415 4.0 27.2 1.0 HB2 B:ALA418 4.0 33.7 1.0 HH21 A:ARG588 4.1 45.9 0.6 N B:PRO417 4.1 25.1 1.0 CA D:ASP362 4.1 28.5 1.0 HD3 B:PRO417 4.1 31.8 1.0 C B:GLY416 4.1 25.5 1.0 HG2 B:PRO417 4.2 35.3 1.0 C D:ASP361 4.3 38.3 1.0 CA D:ASP361 4.4 33.4 1.0 OD1 D:ASP361 4.4 33.0 1.0 OD1 A:ASP591 4.4 42.2 1.0 CB B:ALA418 4.4 28.1 1.0 N B:ALA418 4.4 25.4 1.0 H D:ARG363 4.5 39.3 1.0 CG B:PRO417 4.5 29.4 1.0 C D:ASP362 4.5 33.4 1.0 CZ A:ARG588 4.6 37.7 0.4 HH12 A:ARG588 4.6 44.5 0.6 N D:ARG363 4.7 32.8 1.0 N B:GLY416 4.7 26.5 1.0 CD1 A:TYR596 4.7 31.8 1.0 HB2 D:ASP362 4.7 43.3 1.0 C B:HIS415 4.8 30.7 1.0 HD13 A:ILE594 4.8 40.8 1.0 CZ A:ARG588 4.8 38.6 0.6 CE2 A:TYR596 4.8 33.6 1.0 CG D:ARG363 4.8 38.4 1.0 HE A:ARG588 4.9 45.5 0.4 HA D:ASP362 4.9 34.2 1.0 HG3 B:PRO417 5.0 35.3 1.0

Sodium binding site 4 out of 8 in the Structural Determination of the Carboxy-Terminal Portion of Atp- Citrate Lyase


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Structural Determination of the Carboxy-Terminal Portion of Atp- Citrate Lyase within 5.0Å range: probe atom residue distance (Å) B Occ B:Na702 b:65.1 occ:1.00 OD2 B:ASP522 2.2 72.7 1.0 H B:THR518 2.5 90.0 1.0 HG1 B:THR518 3.0 79.9 1.0 CG B:ASP522 3.1 69.4 1.0 OG1 B:THR518 3.1 66.6 1.0 OD1 B:ASP522 3.3 68.2 1.0 N B:THR518 3.3 75.0 1.0 HA B:HIS517 3.6 0.6 1.0 HZ3 B:LYS511 3.7 92.2 1.0 ND1 B:HIS517 3.8 94.3 1.0 O B:THR518 3.8 66.3 1.0 HZ1 B:LYS511 3.9 92.2 1.0 C B:THR518 3.9 68.3 1.0 CA B:THR518 4.0 68.6 1.0 HZ2 B:LYS511 4.1 92.2 1.0 CB B:THR518 4.1 67.0 1.0 HE1 B:HIS517 4.1 0.6 1.0 NZ B:LYS511 4.1 76.8 1.0 CE1 B:HIS517 4.3 96.3 1.0 C B:HIS517 4.3 80.6 1.0 CA B:HIS517 4.4 84.7 1.0 HG23 B:THR518 4.4 76.9 1.0 CB B:ASP522 4.4 69.5 1.0 HB2 B:ASP522 4.5 83.5 1.0 O B:LEU516 4.6 74.6 1.0 N B:PRO519 4.7 68.5 1.0 HA B:PRO519 4.8 84.6 1.0 CG B:HIS517 4.8 93.5 1.0 HB3 B:ASP522 4.9 83.5 1.0 CG2 B:THR518 4.9 64.1 1.0 HB B:THR518 4.9 80.5 1.0 HA B:THR518 4.9 82.3 1.0 H B:ASP522 5.0 78.2 1.0

Sodium binding site 5 out of 8 in the Structural Determination of the Carboxy-Terminal Portion of Atp- Citrate Lyase


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Structural Determination of the Carboxy-Terminal Portion of Atp- Citrate Lyase within 5.0Å range: probe atom residue distance (Å) B Occ C:Na704 b:51.4 occ:1.00 OD1 C:ASP434 2.1 47.5 0.7 O A:HOH847 2.2 41.0 1.0 HD22 A:ASN561 2.7 52.5 1.0 H C:MET435 2.7 27.1 1.0 HB3 C:MET435 2.8 27.7 1.0 CG C:ASP434 2.9 34.7 0.7 OD2 C:ASP434 3.0 34.4 0.7 HD3 C:PRO436 3.1 32.0 1.0 HB2 C:MET435 3.2 27.7 1.0 HB3 C:ASP434 3.4 33.4 0.3 CB C:MET435 3.5 23.1 1.0 ND2 A:ASN561 3.5 43.7 1.0 N C:MET435 3.5 22.6 1.0 HB3 A:ASN561 3.6 41.5 1.0 HB2 A:ASN561 3.7 41.5 1.0 HH2 C:TRP576 3.7 37.0 1.0 HE3 C:MET435 3.9 35.5 1.0 CH2 C:TRP576 4.0 30.8 1.0 CD C:PRO436 4.0 26.6 1.0 HD21 A:ASN561 4.0 52.5 1.0 CB A:ASN561 4.0 34.6 1.0 CA C:MET435 4.1 24.8 1.0 HD2 C:PRO436 4.2 32.0 1.0 HZ2 C:TRP576 4.3 32.9 1.0 CB C:ASP434 4.3 27.9 1.0 CZ2 C:TRP576 4.3 27.4 1.0 CG A:ASN561 4.3 41.7 1.0 HA C:ASP434 4.4 29.6 1.0 C C:ASP434 4.5 22.4 1.0 O A:HOH853 4.6 41.3 1.0 CZ3 C:TRP576 4.6 29.9 1.0 CA C:ASP434 4.6 24.6 1.0 HB3 C:ASP434 4.7 33.4 0.7 HG3 C:PRO436 4.7 30.7 1.0 CG C:MET435 4.7 26.9 1.0 CE C:MET435 4.7 29.6 1.0 O A:HIS558 4.7 41.6 1.0 CG C:ASP434 4.8 29.2 0.3 HZ3 C:TRP576 4.8 35.9 1.0 CG C:PRO436 4.8 25.6 1.0 HA C:MET435 4.8 29.8 1.0 HB2 C:ASP434 4.9 33.4 0.7 N C:PRO436 4.9 23.4 1.0 SD C:MET435 4.9 28.1 1.0 HG2 C:PRO436 5.0 30.7 1.0 HB2 C:ASP434 5.0 33.4 0.3

Sodium binding site 6 out of 8 in the Structural Determination of the Carboxy-Terminal Portion of Atp- Citrate Lyase


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Structural Determination of the Carboxy-Terminal Portion of Atp- Citrate Lyase within 5.0Å range: probe atom residue distance (Å) B Occ C:Na705 b:60.1 occ:1.00 OD1 C:ASP434 2.3 27.4 0.3 O C:HOH809 2.6 48.3 1.0 HA C:ASP434 2.9 29.6 1.0 O C:GLY432 3.3 26.9 1.0 HZ2 C:TRP576 3.3 32.9 1.0 CG C:ASP434 3.5 29.2 0.3 CA C:ASP434 3.7 24.6 1.0 N C:ASP434 3.8 23.9 1.0 HB2 C:ASP434 3.8 33.4 0.7 C C:ILE433 3.9 23.3 1.0 O C:ILE433 3.9 24.6 1.0 O C:HOH837 3.9 27.1 1.0 C C:GLY432 4.1 25.9 1.0 HD21 C:ASN580 4.1 38.0 1.0 OD1 C:ASP434 4.1 47.5 0.7 H C:ASP434 4.1 28.7 1.0 CB C:ASP434 4.2 27.9 1.0 CZ2 C:TRP576 4.3 27.4 1.0 CG C:ASP434 4.5 34.7 0.7 OD2 C:ASP434 4.5 30.1 0.3 HA2 C:GLY432 4.5 32.8 1.0 HB3 C:ASP434 4.6 33.4 0.3 N C:ILE433 4.7 23.6 1.0 HA C:ILE433 4.7 31.8 1.0 CA C:ILE433 4.7 26.5 1.0 HE1 C:TRP576 4.8 32.4 1.0 ND2 C:ASN580 4.8 31.7 1.0 HH2 C:TRP576 4.8 37.0 1.0 CA C:GLY432 4.9 27.4 1.0 HB2 C:ASP434 4.9 33.4 0.3 C C:ASP434 5.0 22.4 1.0 O3 C:GOL702 5.0 45.6 1.0

Sodium binding site 7 out of 8 in the Structural Determination of the Carboxy-Terminal Portion of Atp- Citrate Lyase


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of Structural Determination of the Carboxy-Terminal Portion of Atp- Citrate Lyase within 5.0Å range: probe atom residue distance (Å) B Occ D:Na707 b:48.4 occ:1.00 OE1 D:GLU601 2.1 50.3 1.0 O A:HOH817 2.6 32.8 1.0 HG3 A:ARG368 2.6 37.2 1.0 O A:HOH848 2.9 34.1 1.0 HG3 D:GLU601 2.9 41.1 1.0 CD D:GLU601 3.0 39.5 1.0 HG2 D:GLU601 3.1 41.1 1.0 HA3 A:GLY364 3.1 44.5 1.0 CG D:GLU601 3.2 34.3 1.0 CG A:ARG368 3.6 31.0 1.0 H A:GLY364 3.7 42.0 1.0 HG2 A:ARG368 3.9 37.2 1.0 HB2 A:ARG368 4.0 37.2 1.0 CA A:GLY364 4.0 37.1 1.0 OD2 A:ASP361 4.0 34.5 1.0 HB3 A:ASP361 4.0 39.3 1.0 N A:GLY364 4.1 35.0 1.0 OE2 D:GLU601 4.2 49.5 1.0 O A:HOH827 4.2 41.0 1.0 O D:HOH835 4.3 35.6 1.0 HE A:ARG368 4.3 40.7 1.0 HA2 A:GLY364 4.4 44.5 1.0 CB A:ARG368 4.4 31.0 1.0 O D:HOH820 4.4 29.1 1.0 CG A:ASP361 4.4 35.7 1.0 HD2 A:ARG368 4.5 40.4 1.0 CD A:ARG368 4.5 33.7 1.0 NE A:ARG368 4.6 33.9 1.0 CB D:GLU601 4.7 34.5 1.0 CB A:ASP361 4.8 32.7 1.0 HB3 A:ARG368 4.8 37.2 1.0 H A:GLU365 4.9 48.6 1.0

Sodium binding site 8 out of 8 in the Structural Determination of the Carboxy-Terminal Portion of Atp- Citrate Lyase


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 8 of Structural Determination of the Carboxy-Terminal Portion of Atp- Citrate Lyase within 5.0Å range: probe atom residue distance (Å) B Occ D:Na708 b:64.1 occ:1.00 OE1 D:GLU528 2.5 69.5 1.0 O D:HOH802 2.5 56.2 1.0 HD22 D:LEU525 3.3 74.8 1.0 CD D:GLU528 3.3 69.5 1.0 OE2 D:GLU528 3.3 68.9 1.0 HD23 D:LEU525 3.5 74.8 1.0 CD2 D:LEU525 3.7 62.3 1.0 HD21 D:LEU525 3.7 74.8 1.0 HG12 D:VAL503 3.9 65.6 1.0 HB3 D:LEU540 4.2 73.8 1.0 HG11 D:VAL503 4.4 65.6 1.0 HD23 D:LEU540 4.5 71.1 1.0 HG21 D:VAL507 4.6 64.7 1.0 CG1 D:VAL503 4.6 54.7 1.0 CG D:GLU528 4.7 70.2 1.0 H D:LEU540 5.0 77.2 1.0 HG11 D:VAL507 5.0 68.2 1.0

V.H.Nguyen, N.Singh, A.Medina, I.Uson, M.E.Fraser. Identification of the Active Site Residues in Atp-Citrate Lyase'S Carboxy-Terminal Portion. Protein Sci. V. 28 1840 2019.
ISSN: ESSN 1469-896X
PubMed: 31411782
DOI: 10.1002/PRO.3708