Zinc in PDB 8f0v: Lipocalin-Like Milk Protein-2 - E38A Mutant

The structure of Lipocalin-Like Milk Protein-2 - E38A Mutant, PDB code: 8f0v was solved by R.Subramanian, D.Kanagavijayan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	38.18 / 2.95
Space group	P 2 21 21
Cell size a, b, c (Å), α, β, γ (°)	39.771, 52.337, 136.348, 90, 90, 90
R / Rfree (%)	23.5 / 29.4

The binding sites of Zinc atom in the Lipocalin-Like Milk Protein-2 - E38A Mutant (pdb code 8f0v). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the Lipocalin-Like Milk Protein-2 - E38A Mutant, PDB code: 8f0v:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in the Lipocalin-Like Milk Protein-2 - E38A Mutant


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Lipocalin-Like Milk Protein-2 - E38A Mutant within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn204 b:122.6 occ:1.00 OD2 A:ASP53 2.0 101.6 1.0 OE2 A:GLU61 2.0 123.1 1.0 NE2 A:HIS63 2.3 138.4 1.0 O A:HOH302 2.3 71.0 1.0 OD1 A:ASP53 2.5 88.0 1.0 CG A:ASP53 2.5 98.1 1.0 CD A:GLU61 2.9 109.4 1.0 CE1 A:HIS63 3.3 131.6 1.0 CD2 A:HIS63 3.3 125.2 1.0 HD2 A:HIS63 3.4 126.2 1.0 HE1 A:HIS63 3.4 129.7 1.0 OE1 A:GLU61 3.6 120.7 1.0 HG3 A:GLU61 3.6 105.8 1.0 CG A:GLU61 3.9 104.0 1.0 CB A:ASP53 4.0 104.4 1.0 O A:ASP53 4.1 115.0 1.0 HG A:SER55 4.1 142.8 0.0 HB2 A:ASP53 4.2 103.6 1.0 HB3 A:ASP53 4.4 103.6 1.0 ND1 A:HIS63 4.4 118.8 1.0 HG21 A:VAL33 4.4 103.8 1.0 CG A:HIS63 4.4 118.0 1.0 HB2 A:GLU61 4.5 109.1 1.0 OG A:SER55 4.5 140.6 1.0 HG2 A:GLU61 4.6 105.8 1.0 HE3 A:MET78 4.6 117.2 1.0 HG21 A:THR81 4.7 144.6 1.0 HG22 A:VAL33 4.7 103.8 1.0 CB A:GLU61 4.8 106.1 1.0 C A:ASP53 4.9 108.6 1.0

Zinc binding site 2 out of 3 in the Lipocalin-Like Milk Protein-2 - E38A Mutant


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Lipocalin-Like Milk Protein-2 - E38A Mutant within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn205 b:112.3 occ:1.00 NE2 A:HIS103 1.9 78.2 1.0 OE2 A:GLU2 2.0 121.6 1.0 OE1 A:GLU2 2.0 116.6 1.0 CD A:GLU2 2.3 119.9 1.0 CE1 A:HIS103 2.9 77.7 1.0 CD2 A:HIS103 2.9 73.2 1.0 HE1 A:HIS103 3.1 75.8 1.0 HD2 A:HIS103 3.1 72.8 1.0 HE1 A:TYR101 3.3 89.4 1.0 CG A:GLU2 3.8 113.2 1.0 ND1 A:HIS103 3.9 69.5 1.0 CG A:HIS103 4.0 67.1 1.0 HD1 A:TYR101 4.0 84.2 1.0 HA A:GLU2 4.0 112.0 1.0 O A:LYS1 4.0 136.7 1.0 CE1 A:TYR101 4.1 90.3 1.0 HG2 A:GLU2 4.1 114.5 1.0 HG3 A:GLU2 4.2 114.5 1.0 HD2 A:PRO3 4.3 121.2 1.0 CD1 A:TYR101 4.4 82.8 1.0 HB2 A:GLU2 4.6 111.9 1.0 CB A:GLU2 4.6 112.5 1.0 HD1 A:HIS103 4.7 73.7 0.0 CA A:GLU2 4.8 109.2 1.0 HD3 A:PRO3 4.9 121.1 1.0 HA2 A:GLY102 5.0 63.9 1.0

Zinc binding site 3 out of 3 in the Lipocalin-Like Milk Protein-2 - E38A Mutant


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Lipocalin-Like Milk Protein-2 - E38A Mutant within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn206 b:88.1 occ:0.50 NE2 A:HIS150 2.0 72.0 1.0 OE2 A:GLU155 2.1 101.7 1.0 CD A:GLU155 2.9 98.3 1.0 CE1 A:HIS150 2.9 73.0 1.0 CD2 A:HIS150 3.1 74.9 1.0 HE1 A:HIS150 3.1 73.2 1.0 OE1 A:GLU155 3.1 100.7 1.0 HA A:ARG152 3.2 109.4 1.0 HD2 A:HIS150 3.3 75.6 1.0 HB3 A:ARG152 3.6 127.4 1.0 CA A:ARG152 4.0 111.4 1.0 ND1 A:HIS150 4.1 72.5 1.0 CB A:ARG152 4.1 127.1 1.0 HG3 A:ARG152 4.2 141.8 1.0 CG A:HIS150 4.2 81.3 1.0 HG2 A:ARG152 4.2 142.4 1.0 CG A:GLU155 4.3 96.1 1.0 HG3 A:GLU155 4.4 96.3 1.0 CG A:ARG152 4.4 146.2 1.0 N A:ARG152 4.6 95.7 1.0 HD1 A:HIS150 4.8 71.8 0.0 HG2 A:GLU155 4.9 96.2 1.0 C A:CYS151 5.0 92.1 1.0 HB2 A:GLU155 5.0 95.5 1.0

P.R.Santhakumari, K.Dhanabalan, S.Virani, A.S.Hopf-Jannasch, J.B.Benoit, G.Chopra, R.Subramanian. Variability in Phenylalanine Side Chain Conformations Facilitates Broad Substrate Tolerance of Fatty Acid Binding in Cockroach Milk Proteins. Plos One V. 18 80009 2023.
ISSN: ESSN 1932-6203
PubMed: 37384723
DOI: 10.1371/JOURNAL.PONE.0280009