Zinc in PDB 1umy: Bhmt From Rat Liver

All present enzymatic activity of Bhmt From Rat Liver:
2.1.1.5;

The structure of Bhmt From Rat Liver, PDB code: 1umy was solved by B.Gonzalez, M.A.Pajares, J.Sanz-Aparicio, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.40 / 2.50
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	57.830, 149.270, 96.250, 90.00, 92.92, 90.00
R / Rfree (%)	25.3 / 29.1

The binding sites of Zinc atom in the Bhmt From Rat Liver (pdb code 1umy). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Bhmt From Rat Liver, PDB code: 1umy:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Bhmt From Rat Liver


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Bhmt From Rat Liver within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1399 b:72.5 occ:1.00 SG A:CYS217 2.5 55.2 1.0 SG A:CYS299 2.6 44.4 1.0 OH A:TYR160 2.7 58.4 1.0 SG A:CYS300 2.7 41.9 1.0 CB A:CYS217 3.4 52.9 1.0 CZ A:TYR160 3.4 58.8 1.0 CE1 A:TYR160 3.5 59.0 1.0 N A:CYS300 3.5 34.6 1.0 CB A:CYS300 3.6 36.7 1.0 S2 A:BME1400 3.8 68.1 1.0 CB A:CYS299 3.8 38.4 1.0 CA A:CYS300 4.1 36.5 1.0 O A:HOH2001 4.1 41.5 1.0 C A:CYS299 4.4 35.5 1.0 CA A:CYS217 4.5 53.6 1.0 CA A:CYS299 4.6 37.6 1.0 CE2 A:TYR160 4.6 58.8 1.0 CD1 A:TYR160 4.7 58.3 1.0 O A:HOH2004 4.8 33.4 1.0 O A:HOH2044 4.9 50.1 1.0 CD2 A:LEU249 5.0 43.1 1.0

Zinc binding site 2 out of 4 in the Bhmt From Rat Liver


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Bhmt From Rat Liver within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1399 b:67.7 occ:1.00 SG B:CYS300 2.5 41.1 1.0 SG B:CYS217 2.6 63.2 1.0 OH B:TYR160 2.7 49.8 1.0 SG B:CYS299 2.7 44.5 1.0 CE2 B:TYR160 3.3 51.1 1.0 N B:CYS300 3.4 37.2 1.0 CB B:CYS300 3.4 36.9 1.0 CZ B:TYR160 3.4 50.4 1.0 CB B:CYS217 3.4 60.0 1.0 CB B:CYS299 3.9 38.1 1.0 CA B:CYS300 3.9 37.0 1.0 C B:CYS299 4.4 38.3 1.0 O B:HOH2006 4.4 31.5 1.0 C2 B:BME1400 4.5 57.4 1.0 CA B:CYS299 4.6 39.0 1.0 CD2 B:TYR160 4.6 52.0 1.0 CA B:CYS217 4.7 58.5 1.0 CE1 B:TYR160 4.8 48.8 1.0 CD2 B:LEU249 4.9 43.3 1.0

Zinc binding site 3 out of 4 in the Bhmt From Rat Liver


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Bhmt From Rat Liver within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn1406 b:0.1 occ:1.00 OH C:TYR160 2.4 65.2 1.0 SG C:CYS300 2.5 49.1 1.0 O C:HOH2107 2.7 55.8 1.0 SG C:CYS217 2.9 75.4 1.0 CE1 C:TYR160 2.9 64.5 1.0 SG C:CYS299 2.9 48.2 1.0 CZ C:TYR160 3.0 64.7 1.0 CB C:CYS300 3.5 41.3 1.0 N C:CYS300 3.6 41.3 1.0 CB C:CYS217 4.1 69.9 1.0 CA C:CYS300 4.1 41.0 1.0 CB C:CYS299 4.2 42.7 1.0 CD1 C:TYR160 4.3 63.5 1.0 CE2 C:TYR160 4.4 64.2 1.0 C C:CYS299 4.7 41.0 1.0 CA C:CYS299 4.9 41.4 1.0

Zinc binding site 4 out of 4 in the Bhmt From Rat Liver


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Bhmt From Rat Liver within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn1405 b:71.1 occ:1.00 SG D:CYS300 2.4 49.5 1.0 SG D:CYS299 2.5 50.3 1.0 SG D:CYS217 2.5 63.6 1.0 N D:CYS300 2.6 40.0 1.0 CB D:CYS300 2.9 41.9 1.0 OH D:TYR160 3.2 60.3 1.0 CB D:CYS299 3.2 43.0 1.0 CA D:CYS300 3.3 41.1 1.0 C D:CYS299 3.7 41.8 1.0 CA D:CYS299 3.9 42.1 1.0 O D:HOH2073 3.9 42.5 1.0 CB D:CYS217 4.1 62.3 1.0 CZ D:TYR160 4.1 60.4 1.0 CD2 D:LEU249 4.4 45.0 1.0 CA D:CYS217 4.4 62.0 1.0 C D:CYS300 4.6 40.6 1.0 O D:HOH2015 4.7 35.9 1.0 CE2 D:TYR160 4.7 61.0 1.0 O D:CYS299 4.8 42.5 1.0 CE1 D:TYR160 4.9 58.9 1.0 O D:CYS300 4.9 41.4 1.0

B.Gonzalez, M.A.Pajares, M.Martinez-Ripoll, T.L.Blundell, J.Sanz-Aparicio. Crystal Structure of Rat Liver Betaine Homocysteine S-Methyltransferase Reveals New Oligomerization Features and Conformational Changes Upon Substrate Binding. J. Mol. Biol. V. 338 771 2004.
ISSN: ISSN 0022-2836
PubMed: 15099744
DOI: 10.1016/J.JMB.2004.03.005