Zinc in PDB 4rfl: Crystal Structure of G1PDH with Nadph From Methanocaldococcus Jannaschii

All present enzymatic activity of Crystal Structure of G1PDH with Nadph From Methanocaldococcus Jannaschii:
1.1.1.261;

The structure of Crystal Structure of G1PDH with Nadph From Methanocaldococcus Jannaschii, PDB code: 4rfl was solved by V.Carbone, R.S.Ronimus, L.R.Schofield, A.J.Sutherland-Smith, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.68 / 2.20
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	59.391, 72.115, 101.714, 77.62, 79.58, 75.63
R / Rfree (%)	18.5 / 22.5

The structure of Crystal Structure of G1PDH with Nadph From Methanocaldococcus Jannaschii also contains other interesting chemical elements:

Potassium	(K)	4 atoms
Sodium	(Na)	1 atom

The binding sites of Zinc atom in the Crystal Structure of G1PDH with Nadph From Methanocaldococcus Jannaschii (pdb code 4rfl). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Crystal Structure of G1PDH with Nadph From Methanocaldococcus Jannaschii, PDB code: 4rfl:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Crystal Structure of G1PDH with Nadph From Methanocaldococcus Jannaschii


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of G1PDH with Nadph From Methanocaldococcus Jannaschii within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn403 b:30.7 occ:0.50 O A:HOH501 2.0 40.0 1.0 NE2 A:HIS226 2.1 35.3 1.0 OD1 A:ASP148 2.2 38.1 1.0 NE2 A:HIS247 2.3 36.6 1.0 CG A:ASP148 3.0 34.9 1.0 CE1 A:HIS247 3.1 37.5 1.0 CD2 A:HIS226 3.1 35.0 1.0 CE1 A:HIS226 3.1 33.6 1.0 OD2 A:ASP148 3.1 33.9 1.0 O A:HOH538 3.3 36.4 1.0 CD2 A:HIS247 3.4 37.1 1.0 C4N A:NDP401 3.7 36.7 0.8 OD1 A:ASP105 3.8 28.3 1.0 SG A:CYS251 4.1 28.2 1.0 ND1 A:HIS226 4.2 33.9 1.0 CG A:HIS226 4.2 32.7 1.0 ND1 A:HIS247 4.2 34.4 1.0 N7N A:NDP401 4.3 39.2 0.8 CG A:ASP105 4.3 27.6 1.0 OD2 A:ASP105 4.4 31.5 1.0 CG A:HIS247 4.4 30.9 1.0 CB A:ASP148 4.5 30.3 1.0 C3N A:NDP401 4.5 38.2 0.8 C5N A:NDP401 4.5 34.6 0.8 K A:K402 4.6 33.2 1.0 C7N A:NDP401 4.7 41.8 0.8 CA A:ASP148 4.9 28.7 1.0

Zinc binding site 2 out of 4 in the Crystal Structure of G1PDH with Nadph From Methanocaldococcus Jannaschii


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of G1PDH with Nadph From Methanocaldococcus Jannaschii within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn403 b:33.7 occ:0.50 O B:HOH501 2.0 42.1 1.0 NE2 B:HIS226 2.1 33.0 1.0 NE2 B:HIS247 2.2 36.9 1.0 OD1 B:ASP148 2.4 43.0 1.0 CE1 B:HIS247 3.0 37.3 1.0 CE1 B:HIS226 3.0 31.0 1.0 CD2 B:HIS226 3.0 33.0 1.0 CG B:ASP148 3.2 37.2 1.0 CD2 B:HIS247 3.3 36.7 1.0 OD2 B:ASP148 3.3 38.6 1.0 N7N B:NDP401 3.5 37.5 0.6 C4N B:NDP401 3.6 38.7 0.6 OD1 B:ASP105 3.9 28.7 1.0 ND1 B:HIS226 4.1 30.5 1.0 ND1 B:HIS247 4.1 36.0 1.0 CG B:HIS226 4.2 30.1 1.0 SG B:CYS251 4.2 28.9 1.0 C7N B:NDP401 4.3 40.4 0.6 C3N B:NDP401 4.3 38.5 0.6 CG B:HIS247 4.3 33.7 1.0 CG B:ASP105 4.4 30.3 1.0 OD2 B:ASP105 4.4 32.7 1.0 O B:HOH557 4.5 37.3 1.0 C5N B:NDP401 4.6 37.5 0.6 CB B:ASP148 4.6 28.7 1.0 K B:K402 4.8 34.2 1.0 CB B:ASN104 4.9 32.6 1.0

Zinc binding site 3 out of 4 in the Crystal Structure of G1PDH with Nadph From Methanocaldococcus Jannaschii


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of G1PDH with Nadph From Methanocaldococcus Jannaschii within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn403 b:36.6 occ:0.50 O C:HOH501 2.0 46.2 1.0 NE2 C:HIS226 2.1 40.2 1.0 OD1 C:ASP148 2.3 42.7 1.0 NE2 C:HIS247 2.3 48.4 1.0 CE1 C:HIS226 3.0 35.9 1.0 CE1 C:HIS247 3.1 46.0 1.0 CD2 C:HIS226 3.1 38.4 1.0 CG C:ASP148 3.2 34.8 1.0 O C:HOH567 3.2 35.2 1.0 OD2 C:ASP148 3.4 44.7 1.0 CD2 C:HIS247 3.4 46.1 1.0 C4N C:NDP401 4.0 36.6 0.6 OD1 C:ASP105 4.1 33.3 1.0 ND1 C:HIS226 4.2 36.6 1.0 CG C:HIS226 4.2 35.2 1.0 ND1 C:HIS247 4.3 42.2 1.0 SG C:CYS251 4.3 34.8 1.0 C5N C:NDP401 4.4 36.9 0.6 CG C:HIS247 4.5 40.6 1.0 K C:K402 4.5 45.1 1.0 CB C:ASP148 4.6 33.0 1.0 OD2 C:ASP105 4.6 40.6 1.0 CG C:ASP105 4.6 34.4 1.0 CB C:ASN104 5.0 40.0 1.0 O7N C:NDP401 5.0 40.8 0.6

Zinc binding site 4 out of 4 in the Crystal Structure of G1PDH with Nadph From Methanocaldococcus Jannaschii


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of G1PDH with Nadph From Methanocaldococcus Jannaschii within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn403 b:39.8 occ:0.50 O D:HOH501 2.0 31.6 0.5 NE2 D:HIS226 2.0 37.4 1.0 OD1 D:ASP148 2.1 47.0 1.0 NE2 D:HIS247 2.5 43.8 1.0 CE1 D:HIS226 2.9 33.8 1.0 CD2 D:HIS226 3.0 38.1 1.0 CG D:ASP148 3.1 36.9 1.0 CE1 D:HIS247 3.4 50.1 1.0 OD2 D:ASP148 3.4 38.6 1.0 CD2 D:HIS247 3.4 43.6 1.0 O D:HOH529 3.4 36.8 1.0 C4N D:NDP401 3.7 40.6 0.6 OD1 D:ASP105 3.9 31.5 1.0 ND1 D:HIS226 4.0 31.8 1.0 O7N D:NDP401 4.0 39.6 0.6 SG D:CYS251 4.1 31.1 1.0 CG D:HIS226 4.1 35.2 1.0 OD2 D:ASP105 4.3 27.6 1.0 CG D:ASP105 4.4 29.0 1.0 CB D:ASP148 4.4 37.4 1.0 ND1 D:HIS247 4.5 45.5 1.0 C3N D:NDP401 4.5 41.2 0.6 CG D:HIS247 4.5 44.7 1.0 C5N D:NDP401 4.5 37.9 0.6 C7N D:NDP401 4.6 43.9 0.6 K D:K402 4.6 35.5 1.0 CA D:ASP148 4.8 36.0 1.0

V.Carbone, L.R.Schofield, Y.Zhang, C.Sang, D.Dey, I.M.Hannus, W.F.Martin, A.J.Sutherland-Smith, R.S.Ronimus. Structure and Evolution of the Archaeal Lipid Synthesis Enzyme Sn-Glycerol-1-Phosphate Dehydrogenase. J.Biol.Chem. V. 290 21690 2015.
ISSN: ISSN 0021-9258
PubMed: 26175150
DOI: 10.1074/JBC.M115.647461