Zinc in PDB 9f5b: Identification of Zinc Ions in LMO4.

The structure of Identification of Zinc Ions in LMO4., PDB code: 9f5b was solved by K.El Omari, I.Forsyth, E.J.Mancini, A.Wagner, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	53.53 / 1.80
Space group	P 3 1 2
Cell size a, b, c (Å), α, β, γ (°)	61.816, 61.816, 93.396, 90, 90, 120
R / Rfree (%)	19.8 / 23.4

The binding sites of Zinc atom in the Identification of Zinc Ions in LMO4. (pdb code 9f5b). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Identification of Zinc Ions in LMO4., PDB code: 9f5b:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Identification of Zinc Ions in LMO4.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Identification of Zinc Ions in LMO4. within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn400 b:27.9 occ:1.00 ND1 A:HIS44 2.2 30.8 1.0 SG A:CYS47 2.2 28.7 1.0 SG A:CYS23 2.3 25.4 1.0 SG A:CYS26 2.4 31.5 1.0 CB A:CYS23 3.0 24.1 1.0 CE1 A:HIS44 3.2 27.6 1.0 CB A:CYS47 3.2 29.3 1.0 CG A:HIS44 3.2 28.3 1.0 CB A:CYS26 3.3 32.1 1.0 CB A:HIS44 3.5 25.7 1.0 N A:CYS26 3.7 32.1 1.0 N A:HIS44 4.0 23.9 1.0 CA A:CYS26 4.1 31.6 1.0 O A:HOH552 4.1 58.7 1.0 NE2 A:HIS44 4.3 28.0 1.0 CD2 A:HIS44 4.3 26.5 1.0 CA A:HIS44 4.4 23.3 1.0 CA A:CYS23 4.5 29.5 1.0 NH1 A:ARG46 4.6 35.5 1.0 CA A:CYS47 4.6 28.9 1.0 C A:GLY25 4.6 38.6 1.0 O A:HOH612 4.7 40.4 1.0 NH2 A:ARG46 4.7 36.0 1.0 CZ A:ARG46 4.8 36.8 1.0 CA A:GLY25 4.8 30.1 1.0 N A:GLY25 4.9 26.8 1.0 C A:CYS26 4.9 32.3 1.0 O A:HIS44 5.0 23.9 1.0 N A:CYS47 5.0 27.7 1.0 C A:CYS23 5.0 31.8 1.0

Zinc binding site 2 out of 4 in the Identification of Zinc Ions in LMO4.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Identification of Zinc Ions in LMO4. within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn401 b:27.7 occ:1.00 OD2 A:ASP76 2.0 28.9 1.0 SG A:CYS53 2.3 30.2 1.0 SG A:CYS73 2.3 27.7 1.0 SG A:CYS50 2.4 25.9 1.0 CG A:ASP76 3.0 29.1 1.0 CB A:CYS50 3.2 23.6 1.0 CB A:CYS53 3.3 31.0 1.0 CB A:CYS73 3.4 29.1 1.0 CB A:ASP76 3.5 25.7 1.0 N A:CYS53 3.7 27.4 1.0 O A:HOH526 3.8 53.5 1.0 N A:CYS73 3.9 24.2 1.0 CA A:CYS53 4.0 27.7 1.0 OD1 A:ASP76 4.2 31.2 1.0 CA A:CYS73 4.3 27.9 1.0 N A:ASP76 4.4 30.5 1.0 O A:HOH603 4.5 42.8 1.0 CA A:ASP76 4.6 26.4 1.0 CB A:SER52 4.6 29.8 1.0 CA A:CYS50 4.6 22.9 1.0 C A:CYS53 4.7 29.6 1.0 C A:SER52 4.8 34.1 1.0 CB A:ALA55 4.9 23.9 1.0 C A:CYS73 4.9 30.9 1.0 N A:GLN54 5.0 26.7 1.0

Zinc binding site 3 out of 4 in the Identification of Zinc Ions in LMO4.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Identification of Zinc Ions in LMO4. within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn402 b:56.2 occ:1.00 OD2 A:ASP140 2.1 56.6 1.0 SG A:CYS118 2.3 60.4 1.0 SG A:CYS137 2.3 54.6 1.0 SG A:CYS115 2.4 55.2 1.0 CG A:ASP140 3.1 55.5 1.0 CB A:CYS115 3.2 55.6 1.0 CB A:CYS118 3.2 61.3 1.0 CB A:CYS137 3.3 49.9 1.0 CB A:ASP140 3.5 55.3 1.0 N A:CYS118 3.8 55.8 1.0 N A:CYS137 3.9 45.6 1.0 CA A:CYS118 4.1 60.9 1.0 CA A:CYS137 4.1 42.3 1.0 OD1 A:ASP140 4.2 64.0 1.0 N A:ASP140 4.5 57.1 1.0 CA A:ASP140 4.6 47.6 1.0 CA A:CYS115 4.7 47.5 1.0 C A:CYS137 4.7 51.5 1.0 CB A:THR117 4.8 60.8 1.0 O A:CYS137 4.8 47.5 1.0 C A:CYS118 4.8 61.0 1.0 C A:THR117 4.9 60.9 1.0 N A:ARG119 4.9 63.5 1.0 CB A:ASN120 5.0 56.1 1.0

Zinc binding site 4 out of 4 in the Identification of Zinc Ions in LMO4.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Identification of Zinc Ions in LMO4. within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn403 b:48.3 occ:1.00 ND1 A:HIS109 2.3 56.8 1.0 SG A:CYS112 2.3 47.6 1.0 SG A:CYS90 2.3 51.2 1.0 SG A:CYS87 2.4 48.4 1.0 CB A:CYS87 3.1 39.7 1.0 CB A:CYS112 3.1 43.7 1.0 CG A:HIS109 3.2 52.3 1.0 CB A:CYS90 3.2 54.7 1.0 CE1 A:HIS109 3.3 53.2 1.0 CB A:HIS109 3.4 49.6 1.0 N A:CYS90 3.8 52.9 1.0 N A:HIS109 4.0 43.3 1.0 CA A:CYS90 4.1 47.6 1.0 CD2 A:HIS109 4.4 51.3 1.0 CA A:HIS109 4.4 45.6 1.0 NE2 A:HIS109 4.4 56.7 1.0 CA A:CYS112 4.5 46.1 1.0 CA A:CYS87 4.6 45.5 1.0 CB A:ALA89 4.6 46.4 1.0 C A:ALA89 4.8 51.4 1.0 C A:CYS90 4.9 45.6 1.0 N A:CYS112 4.9 52.2 1.0

K.El Omari, I.Forsyth, R.Duman, C.M.Orr, V.Mykhaylyk, E.J.Mancini, A.Wagner. Utilizing Anomalous Signals For Element Identification in Macromolecular Crystallography. Acta Crystallogr D Struct 2024BIOL.
ISSN: ISSN 2059-7983
PubMed: 39291627
DOI: 10.1107/S2059798324008659