Zinc in PDB 5dmm: Crystal Structure of the Homocysteine Methyltransferase Mmum From Escherichia Coli, Metallated Form

All present enzymatic activity of Crystal Structure of the Homocysteine Methyltransferase Mmum From Escherichia Coli, Metallated Form:
2.1.1.10;

The structure of Crystal Structure of the Homocysteine Methyltransferase Mmum From Escherichia Coli, Metallated Form, PDB code: 5dmm was solved by K.Li, G.Li, L.M.T.Bradbury, H.D.Andrew, S.D.Bruner, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	24.23 / 1.78
Space group	I 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	78.949, 85.924, 87.662, 90.00, 90.00, 90.00
R / Rfree (%)	18.3 / 20.5

The binding sites of Zinc atom in the Crystal Structure of the Homocysteine Methyltransferase Mmum From Escherichia Coli, Metallated Form (pdb code 5dmm). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the Crystal Structure of the Homocysteine Methyltransferase Mmum From Escherichia Coli, Metallated Form, PDB code: 5dmm:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in the Crystal Structure of the Homocysteine Methyltransferase Mmum From Escherichia Coli, Metallated Form


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 the Homocysteine Methyltransferase Mmum From Escherichia Coli, Metallated Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn501 b:51.1 occ:0.57 SG A:CYS295 2.0 29.1 1.0 SG A:CYS229 2.5 50.3 1.0 SD A:HCS505 2.8 38.4 0.8 CB A:CYS229 2.9 25.0 1.0 SG A:CYS296 3.2 46.4 1.0 CB A:CYS295 3.2 17.5 1.0 CA A:CYS229 3.4 19.7 1.0 OD1 A:ASN255 3.5 26.7 1.0 CG A:HCS505 3.6 35.3 0.8 N A:CYS296 3.6 19.6 1.0 S2 A:BME504 3.9 62.5 1.0 N A:CYS229 4.0 18.9 1.0 CB A:CYS296 4.1 30.2 1.0 CA A:CYS295 4.2 19.1 1.0 O A:HOH764 4.2 34.8 1.0 CB A:HCS505 4.2 34.4 0.8 C A:CYS295 4.4 20.7 1.0 CA A:CYS296 4.4 24.7 1.0 ND2 A:ASN228 4.5 16.7 1.0 CG A:ASN255 4.6 26.8 1.0 C A:CYS229 4.7 24.9 1.0 OH A:TYR135 4.8 54.8 1.0

Zinc binding site 2 out of 3 in the Crystal Structure of the Homocysteine Methyltransferase Mmum From Escherichia Coli, Metallated Form


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 the Homocysteine Methyltransferase Mmum From Escherichia Coli, Metallated Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn502 b:17.0 occ:0.35 NE2 A:HIS140 2.0 25.9 1.0 OD1 A:ASP138 2.0 34.9 1.0 CE1 A:HIS140 3.0 24.6 1.0 CG A:ASP138 3.0 37.7 1.0 CD2 A:HIS140 3.1 26.8 1.0 OD2 A:ASP138 3.3 39.8 1.0 ND1 A:HIS140 4.1 26.8 1.0 CG A:HIS140 4.2 25.1 1.0 CB A:ASP138 4.4 29.8 1.0 C A:ASP138 4.6 26.2 1.0 O A:ASP138 4.7 26.7 1.0 CA A:ASP138 4.7 26.7 1.0

Zinc binding site 3 out of 3 in the Crystal Structure of the Homocysteine Methyltransferase Mmum From Escherichia Coli, Metallated Form


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of the Homocysteine Methyltransferase Mmum From Escherichia Coli, Metallated Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn503 b:24.3 occ:0.55 OE1 A:GLU144 2.1 32.9 1.0 O A:HOH741 2.1 25.6 1.0 O A:HOH738 2.5 22.6 1.0 CD A:GLU144 2.9 35.7 1.0 OE2 A:GLU144 3.0 31.7 1.0 CB A:SER142 3.9 22.2 1.0 N A:VAL143 4.2 22.5 1.0 CG A:GLU144 4.3 24.8 1.0 N A:GLU144 4.5 21.1 1.0 CB A:VAL143 4.7 27.6 1.0 OG A:SER142 4.7 23.0 1.0 CA A:SER142 4.8 22.2 1.0 CB A:GLU144 4.9 21.9 1.0 C A:SER142 4.9 21.9 1.0 CA A:VAL143 4.9 24.6 1.0

K.Li, G.Li, L.M.Bradbury, A.D.Hanson, S.D.Bruner. Crystal Structure of the Homocysteine Methyltransferase Mmum From Escherichia Coli. Biochem.J. V. 473 277 2016.
ISSN: ESSN 1470-8728
PubMed: 26564203
DOI: 10.1042/BJ20150980