Chlorine in PDB 5dn9: Crystal Structure of Candida Boidinii Formate Dehydrogenase Complexed with Nad+ and Azide

All present enzymatic activity of Crystal Structure of Candida Boidinii Formate Dehydrogenase Complexed with Nad+ and Azide:
1.2.1.2;

The structure of Crystal Structure of Candida Boidinii Formate Dehydrogenase Complexed with Nad+ and Azide, PDB code: 5dn9 was solved by Q.Guo, L.Gakhar, K.Wichersham, K.Francis, A.Vardi-Kilshtain, D.T.Major, C.M.Cheatum, A.Kohen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	41.98 / 1.50
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	50.931, 116.617, 63.208, 90.00, 106.90, 90.00
R / Rfree (%)	13.8 / 16.9

The binding sites of Chlorine atom in the Crystal Structure of Candida Boidinii Formate Dehydrogenase Complexed with Nad+ and Azide (pdb code 5dn9). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 2 binding sites of Chlorine where determined in the Crystal Structure of Candida Boidinii Formate Dehydrogenase Complexed with Nad+ and Azide, PDB code: 5dn9:
Jump to Chlorine binding site number: 1; 2;

Chlorine binding site 1 out of 2 in the Crystal Structure of Candida Boidinii Formate Dehydrogenase Complexed with Nad+ and Azide


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Crystal Structure of Candida Boidinii Formate Dehydrogenase Complexed with Nad+ and Azide within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl503 b:19.8 occ:1.00 HE1 A:HIS232 2.5 11.2 1.0 H61A A:NAD501 2.7 12.5 1.0 O A:HOH1058 3.0 30.1 1.0 HA3 A:GLY234 3.0 11.0 1.0 O A:HOH1016 3.0 19.4 1.0 O A:HOH945 3.4 38.8 1.0 CE1 A:HIS232 3.4 9.3 1.0 HE2 A:TYR196 3.5 10.5 1.0 N6A A:NAD501 3.5 10.4 1.0 HA2 A:GLY359 3.7 16.8 1.0 HD2 A:TYR196 3.8 11.4 1.0 O A:HOH604 3.8 34.3 1.0 H62A A:NAD501 3.9 12.5 1.0 CA A:GLY234 3.9 9.2 1.0 CE2 A:TYR196 4.0 8.8 1.0 HZ1 A:LYS360 4.1 52.3 1.0 HZ3 A:LYS360 4.1 52.3 1.0 HE2 A:HIS232 4.1 11.4 1.0 NE2 A:HIS232 4.2 9.5 1.0 CD2 A:TYR196 4.2 9.5 1.0 HA2 A:GLY234 4.3 11.0 1.0 HZ2 A:LYS360 4.3 52.3 1.0 NZ A:LYS360 4.3 43.5 1.0 C6A A:NAD501 4.4 8.5 1.0 N7A A:NAD501 4.4 7.8 1.0 C A:GLY234 4.4 12.8 1.0 HA3 A:GLY359 4.4 16.8 1.0 ND1 A:HIS232 4.4 10.4 1.0 O A:GLY234 4.5 11.1 1.0 CA A:GLY359 4.5 14.0 1.0 O A:HOH686 4.5 22.0 1.0 HD1 A:HIS232 4.6 12.4 1.0 HG23 A:THR235 4.6 10.6 1.0 O A:HOH1035 4.7 36.4 1.0 C5A A:NAD501 4.7 7.1 1.0 H A:GLY234 4.7 10.8 1.0 O A:HOH969 4.8 40.2 1.0 H A:LYS360 4.8 27.7 1.0 N A:GLY234 4.9 9.0 1.0

Chlorine binding site 2 out of 2 in the Crystal Structure of Candida Boidinii Formate Dehydrogenase Complexed with Nad+ and Azide


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Crystal Structure of Candida Boidinii Formate Dehydrogenase Complexed with Nad+ and Azide within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl503 b:22.2 occ:1.00 HE1 B:HIS232 2.5 14.1 1.0 H61A B:NAD501 2.7 14.8 1.0 HA3 B:GLY234 2.9 17.3 1.0 O B:HOH1032 3.1 25.8 1.0 O B:HOH1041 3.2 40.3 1.0 O B:HOH614 3.3 33.6 1.0 HE2 B:TYR196 3.4 13.3 1.0 CE1 B:HIS232 3.4 11.8 1.0 N6A B:NAD501 3.5 12.3 1.0 HD2 B:TYR196 3.7 11.5 1.0 HA2 B:GLY359 3.8 18.6 1.0 HZ3 B:LYS360 3.8 53.8 1.0 CA B:GLY234 3.9 14.4 1.0 HZ2 B:LYS360 4.0 53.8 1.0 CE2 B:TYR196 4.0 11.1 1.0 HZ1 B:LYS360 4.0 53.8 1.0 H62A B:NAD501 4.0 14.8 1.0 HE2 B:HIS232 4.0 13.2 1.0 NZ B:LYS360 4.1 44.8 1.0 CD2 B:TYR196 4.1 9.6 1.0 NE2 B:HIS232 4.1 11.0 1.0 HA2 B:GLY234 4.2 17.3 1.0 O B:HOH627 4.2 29.3 1.0 C6A B:NAD501 4.4 12.9 1.0 C B:GLY234 4.4 14.3 1.0 ND1 B:HIS232 4.5 11.0 1.0 HA3 B:GLY359 4.5 18.6 1.0 N7A B:NAD501 4.5 8.9 1.0 O B:GLY234 4.5 15.8 1.0 CA B:GLY359 4.6 15.5 1.0 HG23 B:THR235 4.6 12.0 1.0 HD1 B:HIS232 4.6 13.2 1.0 H B:GLY234 4.6 12.2 1.0 O B:HOH689 4.7 24.0 1.0 C5A B:NAD501 4.7 10.1 1.0 N B:GLY234 4.8 10.2 1.0 H B:LYS360 5.0 28.2 1.0 O B:HOH950 5.0 20.1 1.0

Q.Guo, L.Gakhar, K.Wickersham, K.Francis, A.Vardi-Kilshtain, D.T.Major, C.M.Cheatum, A.Kohen. Structural and Kinetic Studies of Formate Dehydrogenase From Candida Boidinii. Biochemistry V. 55 2760 2016.
ISSN: ISSN 0006-2960
PubMed: 27100912
DOI: 10.1021/ACS.BIOCHEM.6B00181