Zinc in PDB 9jev: Crystal Structure of A Cupin Protein (TM1459) in Zinc (Zn) Substituted Form

The structure of Crystal Structure of A Cupin Protein (TM1459) in Zinc (Zn) Substituted Form, PDB code: 9jev was solved by N.Fujieda, H.Ichihashi, G.Kurisu, S.Itoh, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.00 / 1.12
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	50.598, 57.871, 74.65, 90, 90, 90
R / Rfree (%)	n/a / n/a

The binding sites of Zinc atom in the Crystal Structure of A Cupin Protein (TM1459) in Zinc (Zn) Substituted Form (pdb code 9jev). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Crystal Structure of A Cupin Protein (TM1459) in Zinc (Zn) Substituted Form, PDB code: 9jev:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of A Cupin Protein (TM1459) in Zinc (Zn) Substituted 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 A Cupin Protein (TM1459) in Zinc (Zn) Substituted Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1201 b:10.3 occ:0.91 NE2 A:HIS54 2.1 10.9 1.0 NE2 A:HIS92 2.1 11.3 1.0 NE2 A:HIS58 2.1 11.6 1.0 NE2 A:HIS52 2.2 11.6 1.0 O A:HOH1387 2.2 13.4 1.0 O A:HOH1388 2.2 13.5 1.0 CE1 A:HIS92 3.0 10.2 1.0 CE1 A:HIS54 3.0 9.8 1.0 CE1 A:HIS52 3.1 12.9 1.0 CD2 A:HIS58 3.1 10.7 1.0 CE1 A:HIS58 3.1 12.9 1.0 HE1 A:HIS92 3.2 12.2 1.0 HE1 A:HIS52 3.2 15.5 1.0 HE1 A:HIS54 3.2 11.8 1.0 CD2 A:HIS54 3.2 10.3 1.0 CD2 A:HIS92 3.2 11.5 1.0 HD2 A:HIS58 3.3 12.9 1.0 CD2 A:HIS52 3.3 12.3 1.0 HE1 A:HIS58 3.3 15.4 1.0 HD2 A:HIS54 3.4 12.4 1.0 HD2 A:HIS92 3.4 13.8 1.0 HD2 A:HIS52 3.5 14.8 1.0 ND1 A:HIS92 4.2 10.4 1.0 O A:HOH1414 4.2 19.9 1.0 ND1 A:HIS54 4.2 10.3 1.0 ND1 A:HIS52 4.2 12.8 1.0 ND1 A:HIS58 4.3 11.4 1.0 CG A:HIS54 4.3 9.8 1.0 CG A:HIS58 4.3 11.2 1.0 O A:HOH1439 4.3 25.4 1.0 CG A:HIS92 4.3 10.3 1.0 O A:HOH1385 4.4 13.6 1.0 O A:HOH1329 4.4 24.5 1.0 CG A:HIS52 4.4 11.9 1.0 O A:HOH1369 4.5 35.8 1.0 HE2 A:PHE94 4.5 17.8 1.0 HE1 A:TRP56 4.9 13.4 1.0 HD1 A:HIS92 4.9 12.4 1.0 HD1 A:HIS52 5.0 15.4 1.0 HD1 A:HIS54 5.0 12.3 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of A Cupin Protein (TM1459) in Zinc (Zn) Substituted 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 A Cupin Protein (TM1459) in Zinc (Zn) Substituted Form within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn2201 b:10.8 occ:0.90 NE2 B:HIS92 2.1 11.0 1.0 NE2 B:HIS58 2.1 11.6 1.0 NE2 B:HIS54 2.1 11.3 1.0 NE2 B:HIS52 2.1 13.1 1.0 O B:HOH2398 2.2 17.3 1.0 O B:HOH2389 2.2 16.5 1.0 CE1 B:HIS92 3.0 10.4 1.0 CE1 B:HIS52 3.1 13.7 1.0 CE1 B:HIS54 3.1 11.7 1.0 CE1 B:HIS58 3.1 13.6 1.0 CD2 B:HIS58 3.1 11.6 1.0 CD2 B:HIS92 3.2 11.4 1.0 HE1 B:HIS92 3.2 12.5 1.0 HE1 B:HIS54 3.2 14.1 1.0 HE1 B:HIS52 3.2 16.5 1.0 CD2 B:HIS52 3.2 13.4 1.0 CD2 B:HIS54 3.2 13.0 1.0 HE1 B:HIS58 3.3 16.3 1.0 HD2 B:HIS58 3.3 13.9 1.0 HD2 B:HIS92 3.4 13.7 1.0 HD2 B:HIS52 3.4 16.1 1.0 HD2 B:HIS54 3.4 15.6 1.0 ND1 B:HIS92 4.2 10.6 1.0 ND1 B:HIS52 4.2 13.4 1.0 ND1 B:HIS54 4.2 13.2 1.0 ND1 B:HIS58 4.2 14.3 1.0 O B:HOH2367 4.3 17.3 1.0 CG B:HIS92 4.3 10.8 1.0 CG B:HIS58 4.3 12.2 1.0 CG B:HIS52 4.3 12.1 1.0 CG B:HIS54 4.3 11.7 1.0 HE2 B:PHE94 4.5 14.6 1.0 O B:HOH2394 4.5 20.3 0.5 HE1 B:TRP56 4.9 16.2 1.0 HD1 B:HIS92 4.9 12.7 1.0 HD1 B:HIS52 5.0 16.1 1.0 HD1 B:HIS54 5.0 15.9 1.0

N.Fujieda, K.I.Ishihama, H.Ichihashi, S.Yanagisawa, G.Kurisu, S.Itoh. Unusual Self-Hydroxylation in 4-Histidine Tetrad-Supporting Nonheme Iron Center. Chem Asian J 01191 2025.
ISSN: ESSN 1861-471X
PubMed: 40260495
DOI: 10.1002/ASIA.202401191