Zinc in PDB 2yx1: Crystal Structure of M.Jannaschii Trna M1G37 Methyltransferase

The structure of Crystal Structure of M.Jannaschii Trna M1G37 Methyltransferase, PDB code: 2yx1 was solved by S.Goto-Ito, T.Ito, R.Ishii, Y.Bessho, S.Yokoyama, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.90 / 2.20
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	62.000, 69.790, 87.150, 90.00, 96.07, 90.00
R / Rfree (%)	22.4 / 27.6

The binding sites of Zinc atom in the Crystal Structure of M.Jannaschii Trna M1G37 Methyltransferase (pdb code 2yx1). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 10 binding sites of Zinc where determined in the Crystal Structure of M.Jannaschii Trna M1G37 Methyltransferase, PDB code: 2yx1:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 10 in the Crystal Structure of M.Jannaschii Trna M1G37 Methyltransferase


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 M.Jannaschii Trna M1G37 Methyltransferase within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn501 b:33.8 occ:1.00 OE1 A:GLU230 2.0 32.9 1.0 ND1 A:HIS227 2.1 14.2 1.0 O A:HOH632 2.3 38.6 1.0 CE1 A:HIS227 3.0 31.4 1.0 CG A:HIS227 3.1 28.9 1.0 CD A:GLU230 3.1 52.5 1.0 CB A:HIS227 3.5 30.2 1.0 OE2 A:GLU230 3.6 39.2 1.0 CA A:HIS227 3.7 28.1 1.0 NE2 A:HIS227 4.1 21.6 1.0 CD2 A:HIS227 4.2 25.6 1.0 CG A:GLU230 4.4 41.0 1.0 N A:HIS227 4.5 26.2 1.0 O A:HOH579 4.6 44.6 1.0 CB A:GLU230 4.7 35.6 1.0 C A:HIS227 4.9 33.8 1.0

Zinc binding site 2 out of 10 in the Crystal Structure of M.Jannaschii Trna M1G37 Methyltransferase


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 M.Jannaschii Trna M1G37 Methyltransferase within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn502 b:31.5 occ:1.00 ND1 A:HIS243 2.1 31.5 1.0 O A:HOH505 2.5 21.5 1.0 O A:HOH625 2.5 21.9 1.0 CE1 A:HIS243 3.0 41.5 1.0 CG A:HIS243 3.1 35.2 1.0 CB A:HIS243 3.4 32.0 1.0 CA A:HIS243 3.7 25.2 1.0 O A:HOH630 4.0 48.8 1.0 O A:GLU242 4.1 21.2 1.0 NE2 A:HIS243 4.1 42.7 1.0 CD2 A:HIS243 4.2 31.8 1.0 N A:HIS243 4.5 21.8 1.0 C A:GLU242 4.7 25.0 1.0 C A:HIS243 4.8 29.7 1.0 O A:HIS243 5.0 30.9 1.0

Zinc binding site 3 out of 10 in the Crystal Structure of M.Jannaschii Trna M1G37 Methyltransferase


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 M.Jannaschii Trna M1G37 Methyltransferase within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn503 b:77.3 occ:1.00 O A:PHE303 2.2 44.7 1.0 SG A:CYS307 2.4 42.7 1.0 SG A:CYS309 2.5 42.9 1.0 O A:CYS307 2.6 30.8 1.0 C A:PHE303 2.9 36.7 1.0 C A:CYS307 3.0 26.5 1.0 CB A:CYS309 3.2 39.8 1.0 N A:CYS307 3.4 28.8 1.0 CA A:CYS307 3.5 27.2 1.0 CB A:CYS307 3.5 38.9 1.0 N A:CYS309 3.7 44.9 1.0 N A:GLU304 3.7 41.9 1.0 CA A:PHE303 3.7 36.8 1.0 CB A:PHE303 3.7 38.3 1.0 CA A:GLU304 3.9 47.4 1.0 N A:ASP308 3.9 32.9 1.0 C A:ASP308 4.0 44.8 1.0 CA A:CYS309 4.0 39.0 1.0 CA A:ASP308 4.3 42.2 1.0 C A:GLU304 4.3 45.3 1.0 CD2 A:PHE303 4.4 30.4 1.0 C A:LYS306 4.4 37.4 1.0 O A:GLU304 4.5 48.3 1.0 O A:HOH616 4.5 41.9 1.0 CG A:PHE303 4.6 33.1 1.0 O A:ASP308 4.6 41.8 1.0 N A:LYS306 4.8 45.9 1.0 CA A:LYS306 5.0 39.8 1.0

Zinc binding site 4 out of 10 in the Crystal Structure of M.Jannaschii Trna M1G37 Methyltransferase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of M.Jannaschii Trna M1G37 Methyltransferase within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn504 b:53.4 occ:1.00 NE A:SFG401 2.2 22.4 1.0 CD A:SFG401 3.0 26.0 1.0 CD2 A:TYR177 3.1 71.4 1.0 CE2 A:TYR177 3.2 73.9 1.0 C5' A:SFG401 3.3 26.4 1.0 O A:HOH570 4.2 26.0 1.0 CD A:PRO267 4.2 30.6 1.0 O A:HOH626 4.3 41.4 1.0 CG A:TYR177 4.3 63.2 1.0 O A:ASN265 4.4 18.4 1.0 CG A:SFG401 4.4 19.9 1.0 CZ A:TYR177 4.4 71.1 1.0 O A:HOH596 4.7 36.1 1.0 C4' A:SFG401 4.7 23.6 1.0 CD1 A:LEU266 4.7 21.1 1.0 CA A:LEU266 4.7 30.1 1.0 CB A:SFG401 4.9 20.8 1.0 O A:HOH544 4.9 29.1 1.0 CB A:TYR177 5.0 51.8 1.0

Zinc binding site 5 out of 10 in the Crystal Structure of M.Jannaschii Trna M1G37 Methyltransferase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Crystal Structure of M.Jannaschii Trna M1G37 Methyltransferase within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn505 b:39.1 occ:1.00 ND1 B:HIS11 2.0 40.2 1.0 CE1 B:HIS11 2.9 26.5 1.0 CG B:HIS11 3.0 34.0 1.0 CB B:HIS11 3.3 35.3 1.0 CA B:HIS11 3.8 28.1 1.0 CG2 B:ILE56 4.0 45.8 1.0 O B:HOH550 4.0 34.1 1.0 NE2 B:HIS11 4.0 49.2 1.0 CD2 B:HIS11 4.1 34.0 1.0 CB B:GLN14 4.4 27.9 1.0 CG B:GLN14 4.4 25.9 1.0 O B:HOH514 4.5 23.0 1.0 O B:LYS10 4.7 37.0 1.0 N B:HIS11 4.8 37.8 1.0 O B:HIS11 4.8 37.0 1.0 C B:HIS11 4.8 38.5 1.0

Zinc binding site 6 out of 10 in the Crystal Structure of M.Jannaschii Trna M1G37 Methyltransferase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Crystal Structure of M.Jannaschii Trna M1G37 Methyltransferase within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn506 b:47.9 occ:1.00 OE1 B:GLU230 2.1 47.4 1.0 ND1 B:HIS227 2.5 44.6 1.0 CD B:GLU230 2.9 49.6 1.0 OE2 B:GLU230 3.1 57.7 1.0 CE1 B:HIS227 3.3 46.9 1.0 CG B:HIS227 3.3 36.8 1.0 NZ B:LYS175 3.4 66.7 1.0 CB B:HIS227 3.6 36.0 1.0 CA B:HIS227 3.7 32.5 1.0 CG B:GLU230 4.2 39.6 1.0 O B:HOH544 4.2 53.7 1.0 CE B:LYS175 4.3 60.8 1.0 NE2 B:HIS227 4.3 55.0 1.0 CD2 B:HIS227 4.3 48.7 1.0 CB B:GLU230 4.5 42.5 1.0 N B:HIS227 4.5 33.1 1.0 C B:HIS227 4.9 41.1 1.0 O B:HIS227 5.0 34.0 1.0

Zinc binding site 7 out of 10 in the Crystal Structure of M.Jannaschii Trna M1G37 Methyltransferase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Crystal Structure of M.Jannaschii Trna M1G37 Methyltransferase within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn507 b:70.3 occ:1.00 O B:PHE303 2.1 52.2 1.0 SG B:CYS309 2.4 47.9 1.0 SG B:CYS307 2.6 50.1 1.0 O B:CYS307 2.7 51.6 1.0 C B:PHE303 2.8 50.5 1.0 C B:CYS307 3.1 44.6 1.0 CB B:CYS309 3.1 23.0 1.0 N B:CYS307 3.4 43.6 1.0 CA B:CYS307 3.5 41.2 1.0 N B:GLU304 3.5 49.6 1.0 N B:CYS309 3.6 37.4 1.0 CB B:CYS307 3.6 44.6 1.0 CA B:GLU304 3.7 45.7 1.0 CB B:PHE303 3.7 45.3 1.0 CA B:PHE303 3.7 45.3 1.0 N B:ASP308 3.9 36.1 1.0 CA B:CYS309 3.9 35.3 1.0 C B:ASP308 4.2 43.8 1.0 C B:GLU304 4.2 47.1 1.0 O B:GLU304 4.3 43.4 1.0 CD2 B:PHE303 4.4 43.7 1.0 C B:LYS306 4.5 52.0 1.0 CA B:ASP308 4.5 46.1 1.0 CG B:PHE303 4.6 45.9 1.0 N B:LYS306 4.8 55.2 1.0 O B:ASP308 5.0 46.3 1.0

Zinc binding site 8 out of 10 in the Crystal Structure of M.Jannaschii Trna M1G37 Methyltransferase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Crystal Structure of M.Jannaschii Trna M1G37 Methyltransferase within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn508 b:67.5 occ:1.00 NE B:SFG402 2.4 35.8 1.0 CD B:SFG402 3.3 21.1 1.0 C5' B:SFG402 3.6 20.2 1.0 O B:HOH554 3.8 34.6 1.0 O B:HOH540 3.8 37.0 1.0 CD B:PRO267 4.3 32.9 1.0 CD2 B:TYR177 4.4 64.8 1.0 O B:ASN265 4.5 31.8 1.0 O B:HOH590 4.6 53.5 1.0 CG B:TYR177 4.6 63.6 1.0 CG B:SFG402 4.7 29.8 1.0 CB B:TYR177 4.7 46.0 1.0 CE2 B:TYR177 4.8 66.2 1.0 CG B:PRO267 4.8 42.1 1.0 CD1 B:LEU266 4.9 33.4 1.0 O B:HOH576 4.9 46.8 1.0 CA B:LEU266 4.9 33.4 1.0 C4' B:SFG402 5.0 25.9 1.0

Zinc binding site 9 out of 10 in the Crystal Structure of M.Jannaschii Trna M1G37 Methyltransferase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Crystal Structure of M.Jannaschii Trna M1G37 Methyltransferase within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn509 b:80.2 occ:1.00 NE2 B:HIS271 2.5 48.9 1.0 NZ B:LYS272 2.7 68.6 1.0 O B:HOH560 3.3 54.1 1.0 CE1 B:HIS271 3.3 39.7 1.0 CD2 B:HIS271 3.5 42.3 1.0 CE B:LYS272 3.6 66.6 1.0 CG B:LYS272 4.2 55.0 1.0 CD B:LYS272 4.4 55.7 1.0 ND1 B:HIS271 4.5 37.1 1.0 CG B:HIS271 4.6 39.4 1.0

Zinc binding site 10 out of 10 in the Crystal Structure of M.Jannaschii Trna M1G37 Methyltransferase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of Crystal Structure of M.Jannaschii Trna M1G37 Methyltransferase within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn510 b:71.6 occ:1.00 NZ B:LYS318 2.5 55.3 1.0 CE B:LYS318 3.1 48.9 1.0 O B:HOH590 4.0 53.5 1.0 CD1 B:LEU182 4.1 36.7 1.0 O B:HOH551 4.1 40.3 1.0 CB B:SER179 4.4 39.0 1.0 OG B:SER179 4.5 42.0 1.0 CD2 B:LEU182 4.6 35.4 1.0 CD B:LYS318 4.6 49.6 1.0 CG B:PRO267 4.7 42.1 1.0 O B:HOH554 4.7 34.6 1.0 CG1 B:ILE326 4.9 44.6 1.0 CG B:LEU182 5.0 35.2 1.0

S.Goto-Ito, T.Ito, R.Ishii, Y.Muto, Y.Bessho, S.Yokoyama. Crystal Structure of Archaeal Trna(M(1)G37)Methyltransferase ATRM5. Proteins V. 72 1274 2008.
ISSN: ISSN 0887-3585
PubMed: 18384044
DOI: 10.1002/PROT.22019