Sodium in PDB 7c75: Crystal Structure of Yak Lactoperoxidase with Partially Coordinated Na Ion in the Distal Heme Cavity

The structure of Crystal Structure of Yak Lactoperoxidase with Partially Coordinated Na Ion in the Distal Heme Cavity, PDB code: 7c75 was solved by P.K.Singh, V.Viswanathan, C.Rani, N.Ahmad, P.Sharma, 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)	64.30 / 2.70
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	79.910, 84.830, 98.560, 90.00, 90.00, 90.00
R / Rfree (%)	19.3 / 26.8

The structure of Crystal Structure of Yak Lactoperoxidase with Partially Coordinated Na Ion in the Distal Heme Cavity also contains other interesting chemical elements:

Potassium	(K)	1 atom
Zinc	(Zn)	1 atom
Iron	(Fe)	1 atom
Calcium	(Ca)	1 atom

The binding sites of Sodium atom in the Crystal Structure of Yak Lactoperoxidase with Partially Coordinated Na Ion in the Distal Heme Cavity (pdb code 7c75). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total only one binding site of Sodium was determined in the Crystal Structure of Yak Lactoperoxidase with Partially Coordinated Na Ion in the Distal Heme Cavity, PDB code: 7c75:

Sodium binding site 1 out of 1 in the Crystal Structure of Yak Lactoperoxidase with Partially Coordinated Na Ion in the Distal Heme Cavity


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of Yak Lactoperoxidase with Partially Coordinated Na Ion in the Distal Heme Cavity within 5.0Å range: probe atom residue distance (Å) B Occ A:Na609 b:15.6 occ:0.70 O A:HOH1011 2.3 14.0 1.0 O A:HOH734 2.3 16.0 1.0 NE2 A:HIS109 2.3 16.5 1.0 O1D A:HEM606 2.9 19.3 0.3 O A:HOH703 3.0 15.5 1.0 CE1 A:HIS109 3.2 17.0 1.0 CD2 A:HIS109 3.2 16.5 1.0 O2D A:HEM606 3.4 18.7 0.3 C1A A:HEM606 3.4 18.6 0.3 C1A A:HEM606 3.4 18.7 0.7 NA A:HEM606 3.5 18.5 0.3 CGD A:HEM606 3.5 19.1 0.3 NA A:HEM606 3.5 18.5 0.7 C4D A:HEM606 3.5 18.4 1.0 CHA A:HEM606 3.5 18.1 1.0 ND A:HEM606 3.6 18.8 1.0 NH1 A:ARG255 3.7 23.6 1.0 CD A:ARG255 3.7 22.6 1.0 FE A:HEM606 3.9 18.6 1.0 O A:HOH1086 4.0 26.7 1.0 C2A A:HEM606 4.1 18.8 1.0 C4A A:HEM606 4.1 18.4 1.0 NE A:ARG255 4.2 24.5 1.0 CZ A:ARG255 4.2 24.7 1.0 C3D A:HEM606 4.2 18.8 1.0 ND1 A:HIS109 4.2 16.9 1.0 C1D A:HEM606 4.3 18.8 1.0 CG A:HIS109 4.3 16.1 1.0 C3A A:HEM606 4.5 18.2 1.0 OD1 A:ASP108 4.6 17.7 1.0 C2D A:HEM606 4.6 18.3 1.0 CBD A:HEM606 4.7 19.0 0.7 CBD A:HEM606 4.8 19.0 0.3 CG A:ARG255 4.9 21.6 1.0 CHB A:HEM606 4.9 18.6 1.0 NB A:HEM606 4.9 18.6 1.0 NE2 A:GLN105 4.9 13.4 1.0 CAA A:HEM606 5.0 18.8 1.0

P.K.Singh, V.Viswanathan, C.Rani, N.Ahmad, P.Sharma, P.Kaur, S.Sharma, T.P.Singh. Crystal Structure of Yak Lactoperoxidase with Partially Coordinated Na Ion in the Distal Heme Cavity To Be Published.