Zinc in PDB 2z45: Crystal Structure of Zn-Bound ORF134

The structure of Crystal Structure of Zn-Bound ORF134, PDB code: 2z45 was solved by Y.Tomimoto, K.Ihara, T.Onizuka, S.Kanai, H.Ashida, A.Yokota, S.Tanaka, H.Miyasaka, Y.Yamada, R.Kato, S.Wakatsuki, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 2.15
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	49.295, 67.761, 86.147, 90.00, 90.00, 90.00
R / Rfree (%)	19.2 / 24.7

The binding sites of Zinc atom in the Crystal Structure of Zn-Bound ORF134 (pdb code 2z45). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 9 binding sites of Zinc where determined in the Crystal Structure of Zn-Bound ORF134, PDB code: 2z45:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Zinc binding site 1 out of 9 in the Crystal Structure of Zn-Bound ORF134


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 Zn-Bound ORF134 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1001 b:27.9 occ:1.00 O A:HOH1048 2.0 23.2 1.0 OE2 B:GLU84 2.0 27.3 1.0 OE2 A:GLU88 2.1 26.6 1.0 O B:HOH1011 2.1 20.2 1.0 CD A:GLU88 2.7 24.5 1.0 OE1 A:GLU88 2.8 25.3 1.0 CD B:GLU84 2.8 25.6 1.0 OE1 B:GLU84 2.9 24.3 1.0 O A:GLU84 4.1 16.9 1.0 CB A:PRO87 4.1 21.4 1.0 CG A:GLU88 4.2 23.4 1.0 CG B:GLU84 4.3 24.0 1.0 OE1 A:GLU84 4.3 20.2 1.0 CG A:PRO87 4.3 20.7 1.0 O B:HOH1017 4.6 17.8 1.0 O A:HOH1009 4.7 21.1 1.0 O A:HOH1039 4.7 40.8 1.0 CD A:PRO87 4.8 20.7 1.0 N A:GLU88 4.9 21.8 1.0

Zinc binding site 2 out of 9 in the Crystal Structure of Zn-Bound ORF134


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 Zn-Bound ORF134 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1002 b:21.9 occ:1.00 OE2 B:GLU88 1.9 19.0 1.0 OE2 A:GLU84 2.0 15.6 1.0 O B:HOH1017 2.0 17.8 1.0 OE1 A:GLU84 2.5 20.2 1.0 CD A:GLU84 2.5 17.2 1.0 CD B:GLU88 2.8 20.9 1.0 OE1 B:GLU88 3.0 21.1 1.0 CG A:GLU84 4.0 16.6 1.0 OE1 B:GLU84 4.1 24.3 1.0 CG B:GLU88 4.1 19.0 1.0 O B:GLU84 4.3 22.9 1.0 CB B:PRO87 4.4 17.7 1.0 O A:HOH1016 4.5 27.8 1.0 CG B:PRO87 4.5 19.0 1.0 O A:HOH1048 4.7 23.2 1.0 O B:HOH1042 4.8 34.6 1.0 CD B:PRO87 4.9 18.2 1.0

Zinc binding site 3 out of 9 in the Crystal Structure of Zn-Bound ORF134


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 Zn-Bound ORF134 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1003 b:39.7 occ:1.00 O A:HOH1046 1.9 32.8 1.0 ND1 B:HIS101 2.0 38.6 1.0 OE2 A:GLU76 2.3 28.4 1.0 O A:HOH1011 2.4 24.4 1.0 OE1 A:GLU76 2.8 24.7 1.0 CD A:GLU76 2.9 25.4 1.0 CE1 B:HIS101 2.9 38.8 1.0 CG B:HIS101 3.1 41.1 1.0 O A:HOH1050 3.5 15.6 1.0 CB B:HIS101 3.5 42.7 1.0 CA B:HIS101 4.0 43.2 1.0 NE2 B:HIS101 4.1 38.7 1.0 CD2 B:HIS101 4.2 39.4 1.0 CG A:GLU76 4.3 22.7 1.0 C B:HIS101 4.9 43.7 1.0 O B:HIS101 4.9 43.5 1.0

Zinc binding site 4 out of 9 in the Crystal Structure of Zn-Bound ORF134


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 Zn-Bound ORF134 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1007 b:50.2 occ:1.00 OE1 A:GLU58 2.2 31.6 1.0 O A:HOH1029 2.4 40.7 1.0 OE2 A:GLU58 2.7 31.6 1.0 CD A:GLU58 2.8 30.0 1.0 CG A:GLU58 4.2 25.6 1.0 CD2 A:LEU55 4.3 26.3 1.0 O A:HOH1041 4.6 35.8 1.0 CB A:GLU58 4.8 22.6 1.0

Zinc binding site 5 out of 9 in the Crystal Structure of Zn-Bound ORF134


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 Zn-Bound ORF134 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1008 b:51.1 occ:1.00 NE2 A:HIS48 2.2 32.3 1.0 OE2 A:GLU63 2.3 31.0 1.0 O A:HOH1070 2.5 59.6 1.0 O A:HOH1014 2.5 32.2 1.0 OE1 A:GLU63 2.5 30.1 1.0 CD A:GLU63 2.8 29.1 1.0 CE1 A:HIS48 3.1 32.8 1.0 CD2 A:HIS48 3.2 32.1 1.0 O A:HOH1055 3.7 51.8 1.0 CD1 A:PHE44 3.9 23.1 1.0 CE1 A:PHE44 4.0 24.2 1.0 ND1 A:HIS48 4.2 31.7 1.0 CG A:GLU63 4.3 28.1 1.0 CG A:HIS48 4.3 32.4 1.0 CB A:ARG47 4.7 34.3 1.0 CD A:ARG47 4.8 36.5 1.0 CG A:PHE44 4.9 25.0 1.0 CZ A:PHE44 5.0 24.0 1.0

Zinc binding site 6 out of 9 in the Crystal Structure of Zn-Bound ORF134


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 Zn-Bound ORF134 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1004 b:30.9 occ:1.00 OE2 B:GLU63 2.0 22.9 1.0 NE2 B:HIS48 2.0 20.6 1.0 O B:HOH1055 2.0 22.8 1.0 O B:HOH1050 2.3 52.3 1.0 CD B:GLU63 2.9 25.1 1.0 CE1 B:HIS48 3.0 20.6 1.0 CD2 B:HIS48 3.1 20.6 1.0 OE1 B:GLU63 3.1 25.1 1.0 O B:HOH1048 3.9 38.9 1.0 CE1 B:PHE44 4.1 15.7 1.0 ND1 B:HIS48 4.1 21.2 1.0 CD1 B:PHE44 4.1 16.4 1.0 CG B:HIS48 4.2 21.8 1.0 CG B:GLU63 4.3 23.7 1.0 O B:HOH1024 4.5 40.8 1.0 CG B:ARG47 4.5 29.4 1.0 CD B:ARG47 4.6 34.0 1.0 CB B:ARG47 4.7 26.3 1.0 NE B:ARG47 4.8 37.9 1.0

Zinc binding site 7 out of 9 in the Crystal Structure of Zn-Bound ORF134


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 Zn-Bound ORF134 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1005 b:39.7 occ:1.00 OD1 B:ASP54 1.9 30.6 1.0 OE2 B:GLU58 2.2 30.1 1.0 NE2 A:HIS101 2.3 33.1 1.0 O B:HOH1072 2.4 45.9 1.0 CG B:ASP54 2.8 28.2 1.0 OD2 B:ASP54 3.0 32.7 1.0 CD B:GLU58 3.1 27.5 1.0 CD2 A:HIS101 3.2 31.7 1.0 CE1 A:HIS101 3.3 32.5 1.0 CG B:GLU58 3.4 23.8 1.0 O B:HOH1066 4.0 56.5 1.0 CB B:ASP54 4.2 26.0 1.0 OE1 B:GLU58 4.3 30.2 1.0 ND1 A:HIS101 4.3 32.4 1.0 CG A:HIS101 4.4 31.0 1.0 O B:ASP54 4.4 24.6 1.0 CA B:ASP54 4.7 25.2 1.0 C B:ASP54 4.8 24.4 1.0 CB B:GLU58 4.9 20.8 1.0

Zinc binding site 8 out of 9 in the Crystal Structure of Zn-Bound ORF134


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 Zn-Bound ORF134 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1006 b:47.0 occ:1.00 OE1 B:GLU66 2.2 37.4 1.0 OE2 B:GLU66 2.4 35.8 1.0 CD B:GLU66 2.5 33.6 1.0 O B:HOH1089 2.5 32.2 1.0 O B:HOH1013 2.6 28.3 1.0 CG B:GLU66 3.9 27.9 1.0 CB B:GLU66 4.3 22.9 1.0 OD1 B:ASN64 4.7 18.5 1.0 ND2 B:ASN34 4.9 25.7 1.0 ND2 B:ASN64 4.9 18.2 1.0

Zinc binding site 9 out of 9 in the Crystal Structure of Zn-Bound ORF134


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 Zn-Bound ORF134 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1009 b:64.1 occ:1.00 OE1 B:GLU76 2.1 34.5 1.0 O B:HOH1098 2.2 37.3 1.0 O B:HOH1099 2.3 52.6 1.0 NH1 A:ARG102 2.7 38.4 1.0 CD B:GLU76 2.9 32.6 1.0 OE2 B:GLU76 3.0 35.2 1.0 CZ A:ARG102 3.8 36.6 1.0 NH2 A:ARG102 3.9 36.0 1.0 ND2 A:ASN98 4.0 21.9 1.0 CG B:GLU76 4.3 28.0 1.0 CB A:ASN98 4.3 25.0 1.0 CG A:LYS95 4.7 27.7 1.0 CG A:ASN98 4.7 23.1 1.0 CB B:GLU76 4.8 23.7 1.0 O B:HOH1088 5.0 27.7 1.0 NE A:ARG102 5.0 35.0 1.0 CA A:LYS95 5.0 26.5 1.0

Y.Tomimoto, K.Ihara, T.Onizuka, S.Kanai, H.Ashida, A.Yokota, S.Tanaka, H.Miyasaka, Y.Yamada, R.Kato, S.Wakatsuki. Crystal Structure of ORF134 To Be Published.