Zinc in PDB 3vdf: Crystal Structure of C-Lobe of Bovine Lactoferrin Complexed with Diaminopimelic Acid at 1.46 A Resolution

The structure of Crystal Structure of C-Lobe of Bovine Lactoferrin Complexed with Diaminopimelic Acid at 1.46 A Resolution, PDB code: 3vdf was solved by P.K.Shukla, L.Gautam, M.Sinha, P.Kaur, S.Sharma, T.P.Singh, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	37.87 / 1.46
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	62.212, 50.023, 65.206, 90.00, 107.00, 90.00
R / Rfree (%)	16 / 19.4

The structure of Crystal Structure of C-Lobe of Bovine Lactoferrin Complexed with Diaminopimelic Acid at 1.46 A Resolution also contains other interesting chemical elements:

Iron

(Fe)

1 atom

The binding sites of Zinc atom in the Crystal Structure of C-Lobe of Bovine Lactoferrin Complexed with Diaminopimelic Acid at 1.46 A Resolution (pdb code 3vdf). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Crystal Structure of C-Lobe of Bovine Lactoferrin Complexed with Diaminopimelic Acid at 1.46 A Resolution, PDB code: 3vdf:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of C-Lobe of Bovine Lactoferrin Complexed with Diaminopimelic Acid at 1.46 A Resolution


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 C-Lobe of Bovine Lactoferrin Complexed with Diaminopimelic Acid at 1.46 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn707 b:12.5 occ:1.00 O A:HOH1183 2.0 17.0 1.0 OE2 A:GLU659 2.2 16.1 1.0 OE1 A:GLU659 2.2 12.2 1.0 CD A:GLU659 2.6 15.2 1.0 O A:GLY653 3.7 18.7 1.0 O A:HOH1178 3.9 27.2 1.0 CG A:GLU659 4.0 13.1 1.0 O A:ARG654 4.4 14.1 1.0 O A:HOH1187 4.5 34.7 1.0 CA A:PRO655 4.6 12.4 1.0 N A:THR656 4.8 10.8 1.0 CB A:GLU659 4.8 11.5 1.0 C A:GLY653 4.9 15.7 1.0 C A:ARG654 5.0 14.4 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of C-Lobe of Bovine Lactoferrin Complexed with Diaminopimelic Acid at 1.46 A Resolution


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 C-Lobe of Bovine Lactoferrin Complexed with Diaminopimelic Acid at 1.46 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn708 b:16.7 occ:1.00 NE2 A:HIS588 2.0 15.1 1.0 O2 A:API711 2.1 19.3 0.8 O1 A:API711 2.4 47.4 0.8 C1 A:API711 2.5 24.3 0.8 CE1 A:HIS588 3.0 15.0 1.0 CD2 A:HIS588 3.2 14.4 1.0 C2 A:API711 3.8 35.5 0.8 ND1 A:HIS588 4.2 15.0 1.0 CG A:HIS588 4.2 13.4 1.0 CG2 A:VAL591 4.5 20.5 1.0 C3 A:API711 4.6 38.4 0.8 O A:HOH1131 4.6 17.8 1.0 N2 A:API711 4.7 36.8 0.8

P.K.Shukla, L.Gautam, M.Sinha, P.Kaur, S.Sharma, T.P.Singh. Crystal Structure of C-Lobe of Bovine Lactoferrin Complexed with Diaminopimelic Acid at 1.46 A Resolution To Be Published.