Calcium in PDB 9m26: Crystal Structure of Enterobacter Cloacae Ycdy, A Member of the Redox Enzyme Maturation Protein Family

The structure of Crystal Structure of Enterobacter Cloacae Ycdy, A Member of the Redox Enzyme Maturation Protein Family, PDB code: 9m26 was solved by H.J.Choi, S.J.Lee, J.H.Kim, S.I.Yoon, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.85 / 2.50
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	65.257, 88.69, 82.25, 90, 103.69, 90
R / Rfree (%)	21.3 / 26.6

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 13;

Binding sites:

The binding sites of Calcium atom in the Crystal Structure of Enterobacter Cloacae Ycdy, A Member of the Redox Enzyme Maturation Protein Family (pdb code 9m26). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 13 binding sites of Calcium where determined in the Crystal Structure of Enterobacter Cloacae Ycdy, A Member of the Redox Enzyme Maturation Protein Family, PDB code: 9m26:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Calcium binding site 1 out of 13 in the Crystal Structure of Enterobacter Cloacae Ycdy, A Member of the Redox Enzyme Maturation Protein Family


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of Enterobacter Cloacae Ycdy, A Member of the Redox Enzyme Maturation Protein Family within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca201 b:77.0 occ:1.00 O A:HOH314 2.3 32.0 1.0 OE2 D:GLU180 2.4 28.8 1.0 OE2 A:GLU181 2.5 24.8 1.0 OE2 A:GLU184 2.7 37.0 1.0 OE1 D:GLU180 2.8 25.4 1.0 CD D:GLU180 2.9 22.9 1.0 CD A:GLU181 3.5 21.6 1.0 CD A:GLU184 3.5 29.9 1.0 OE1 A:GLU181 3.7 23.8 1.0 O A:GLU180 3.9 22.4 1.0 CA A:CA204 3.9 23.3 1.0 OE2 D:GLU177 4.2 29.4 1.0 CG A:GLU184 4.2 24.5 1.0 OE1 A:GLU184 4.3 35.4 1.0 CG D:GLU180 4.4 21.9 1.0 C A:GLU180 4.4 18.0 1.0 CB A:GLU180 4.6 15.0 1.0 CB A:GLU184 4.8 19.1 1.0 CA D:CA201 4.8 33.8 1.0 CB D:GLU180 4.8 23.1 1.0 CG A:GLU181 4.8 18.8 1.0 N A:GLU181 5.0 14.9 1.0

Calcium binding site 2 out of 13 in the Crystal Structure of Enterobacter Cloacae Ycdy, A Member of the Redox Enzyme Maturation Protein Family


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of Enterobacter Cloacae Ycdy, A Member of the Redox Enzyme Maturation Protein Family within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca202 b:21.7 occ:1.00 OE1 D:GLU181 2.3 19.2 1.0 OD2 A:ASP176 2.4 21.7 1.0 OE2 A:GLU180 2.6 21.7 1.0 OE2 D:GLU181 2.8 19.1 1.0 OE2 A:GLU177 2.8 28.2 1.0 CD D:GLU181 2.9 18.9 1.0 OE1 A:GLU180 3.0 17.5 1.0 CD A:GLU180 3.1 15.3 1.0 O D:HOH330 3.3 23.2 1.0 OE1 A:GLU177 3.6 30.4 1.0 CD A:GLU177 3.6 28.4 1.0 CG A:ASP176 3.6 19.1 1.0 CA A:CA203 4.0 36.5 1.0 CA D:CA201 4.1 33.8 1.0 O A:HOH336 4.1 23.1 1.0 OD1 A:ASP176 4.1 20.3 1.0 CG D:GLU181 4.4 18.4 1.0 O D:HOH310 4.5 19.6 1.0 CG A:GLU180 4.6 15.0 1.0 CB A:ASP176 4.7 14.3 1.0 O A:ASP176 4.9 17.9 1.0 C A:ASP176 4.9 14.3 1.0 CA A:GLU177 5.0 21.9 1.0 CG A:GLU177 5.0 27.6 1.0 N A:GLU177 5.0 14.3 1.0

Calcium binding site 3 out of 13 in the Crystal Structure of Enterobacter Cloacae Ycdy, A Member of the Redox Enzyme Maturation Protein Family


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of Enterobacter Cloacae Ycdy, A Member of the Redox Enzyme Maturation Protein Family within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca203 b:36.5 occ:1.00 OE2 A:GLU180 2.6 21.7 1.0 O D:HOH310 2.7 19.6 1.0 OD1 A:ASP176 2.7 20.3 1.0 O D:HOH330 3.1 23.2 1.0 CG A:ASP176 3.6 19.1 1.0 CD A:GLU180 3.6 15.3 1.0 OD2 A:ASP176 3.7 21.7 1.0 CA A:CA202 4.0 21.7 1.0 CG A:GLU180 4.0 15.0 1.0 OE1 A:GLU180 4.7 17.5 1.0

Calcium binding site 4 out of 13 in the Crystal Structure of Enterobacter Cloacae Ycdy, A Member of the Redox Enzyme Maturation Protein Family


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystal Structure of Enterobacter Cloacae Ycdy, A Member of the Redox Enzyme Maturation Protein Family within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca204 b:23.3 occ:1.00 OE2 D:GLU180 2.3 28.8 1.0 OE1 A:GLU184 2.6 35.4 1.0 OE2 A:GLU184 3.0 37.0 1.0 CD A:GLU184 3.1 29.9 1.0 CD D:GLU180 3.3 22.9 1.0 CA A:CA201 3.9 77.0 1.0 CG D:GLU180 3.9 21.9 1.0 OE1 D:GLU180 4.3 25.4 1.0 CB D:GLU180 4.5 23.1 1.0 O A:GLU180 4.5 22.4 1.0 CG A:GLU184 4.6 24.5 1.0

Calcium binding site 5 out of 13 in the Crystal Structure of Enterobacter Cloacae Ycdy, A Member of the Redox Enzyme Maturation Protein Family


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Crystal Structure of Enterobacter Cloacae Ycdy, A Member of the Redox Enzyme Maturation Protein Family within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca205 b:23.8 occ:1.00 OE1 A:GLU137 2.3 29.8 1.0 OE2 A:GLU183 2.4 29.4 1.0 OE1 A:GLU179 2.5 25.6 1.0 OE2 A:GLU179 2.7 23.4 1.0 CD A:GLU179 2.9 22.4 1.0 OE2 A:GLU133 3.0 47.6 1.0 CD A:GLU137 3.2 28.2 1.0 CD A:GLU133 3.3 42.9 1.0 OE2 A:GLU137 3.5 31.2 1.0 CD A:GLU183 3.5 27.9 1.0 CG A:GLU133 3.8 28.9 1.0 OE1 A:GLU133 3.9 51.4 1.0 CG A:GLU183 4.1 20.7 1.0 CB A:ASN182 4.3 16.7 1.0 CG A:GLU179 4.4 19.3 1.0 ND2 A:ASN182 4.4 14.1 1.0 CZ2 A:TRP175 4.4 22.6 1.0 OE1 A:GLU183 4.5 28.9 1.0 CG A:GLU137 4.5 25.1 1.0 CH2 A:TRP175 4.5 19.5 1.0 O A:HOH302 4.6 15.7 1.0 O A:HOH306 4.8 31.8 1.0 CG A:ASN182 4.9 14.8 1.0

Calcium binding site 6 out of 13 in the Crystal Structure of Enterobacter Cloacae Ycdy, A Member of the Redox Enzyme Maturation Protein Family


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Crystal Structure of Enterobacter Cloacae Ycdy, A Member of the Redox Enzyme Maturation Protein Family within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca201 b:34.5 occ:1.00 OE2 B:GLU184 2.3 22.3 1.0 OE1 C:GLU180 2.3 26.0 1.0 O C:HOH303 2.4 3.6 1.0 O B:HOH305 2.4 14.6 1.0 OE2 B:GLU181 2.6 19.3 1.0 CD B:GLU184 3.3 25.1 1.0 CD B:GLU181 3.5 22.2 1.0 CD C:GLU180 3.5 23.5 1.0 OE1 B:GLU181 3.6 23.5 1.0 O B:GLU180 3.7 23.4 1.0 CA B:CA204 3.9 20.5 1.0 CG B:GLU184 4.1 24.8 1.0 OE1 B:GLU184 4.1 19.7 1.0 OE2 C:GLU180 4.2 33.3 1.0 OE2 C:GLU177 4.3 30.6 1.0 C B:GLU180 4.4 22.0 1.0 O C:HOH318 4.5 11.7 1.0 CA C:CA201 4.6 53.2 1.0 CG C:GLU180 4.6 19.4 1.0 O C:HOH309 4.6 26.5 1.0 CB B:GLU180 4.8 26.5 1.0 CG B:GLU181 4.9 16.1 1.0 CB B:GLU184 4.9 18.1 1.0 N B:GLU181 4.9 15.6 1.0

Calcium binding site 7 out of 13 in the Crystal Structure of Enterobacter Cloacae Ycdy, A Member of the Redox Enzyme Maturation Protein Family


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Crystal Structure of Enterobacter Cloacae Ycdy, A Member of the Redox Enzyme Maturation Protein Family within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca202 b:17.8 occ:1.00 OE1 B:GLU137 2.4 17.2 1.0 OE2 B:GLU183 2.5 25.2 1.0 OE2 B:GLU179 2.6 23.6 1.0 OE1 B:GLU179 2.7 23.0 1.0 OE2 B:GLU133 2.8 47.4 1.0 CD B:GLU179 3.0 22.1 1.0 CD B:GLU137 3.4 17.4 1.0 CD B:GLU133 3.4 46.6 1.0 CD B:GLU183 3.5 21.8 1.0 OE2 B:GLU137 3.8 19.4 1.0 CG B:GLU183 3.9 17.9 1.0 CG B:GLU133 3.9 35.6 1.0 OE1 B:GLU133 4.1 51.7 1.0 CB B:ASN182 4.4 27.4 1.0 CG B:GLU179 4.5 17.1 1.0 OE1 B:GLU183 4.5 19.1 1.0 ND2 B:ASN182 4.6 14.2 1.0 CZ2 B:TRP175 4.6 16.9 1.0 CH2 B:TRP175 4.6 20.0 1.0 CG B:GLU137 4.7 17.6 1.0 CG B:ASN182 4.9 27.6 1.0

Calcium binding site 8 out of 13 in the Crystal Structure of Enterobacter Cloacae Ycdy, A Member of the Redox Enzyme Maturation Protein Family


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Crystal Structure of Enterobacter Cloacae Ycdy, A Member of the Redox Enzyme Maturation Protein Family within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca203 b:20.0 occ:1.00 OE1 C:GLU181 2.4 25.4 1.0 OE2 B:GLU180 2.6 35.2 1.0 OD2 B:ASP176 2.6 21.8 1.0 OE1 B:GLU180 2.7 32.7 1.0 OE2 C:GLU181 2.7 20.6 1.0 OE2 B:GLU177 2.8 36.2 1.0 CD C:GLU181 2.9 20.8 1.0 CD B:GLU180 3.0 31.2 1.0 CD B:GLU177 3.6 39.5 1.0 OE1 B:GLU177 3.6 53.3 1.0 CG B:ASP176 3.8 25.2 1.0 CA C:CA201 4.0 53.2 1.0 OD1 B:ASP176 4.3 26.3 1.0 CG C:GLU181 4.4 18.0 1.0 CG B:GLU180 4.5 32.0 1.0 OE2 C:GLU180 4.7 33.3 1.0 O B:ASP176 4.9 21.2 1.0 CB B:ASP176 5.0 13.5 1.0 OE1 C:GLU177 5.0 27.8 1.0 CA B:GLU177 5.0 17.5 1.0

Calcium binding site 9 out of 13 in the Crystal Structure of Enterobacter Cloacae Ycdy, A Member of the Redox Enzyme Maturation Protein Family


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 9 of Crystal Structure of Enterobacter Cloacae Ycdy, A Member of the Redox Enzyme Maturation Protein Family within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca204 b:20.5 occ:1.00 OE1 B:GLU184 2.8 19.7 1.0 OE2 B:GLU184 2.9 22.3 1.0 OE1 C:GLU180 3.1 26.0 1.0 CD B:GLU184 3.2 25.1 1.0 CD C:GLU180 3.5 23.5 1.0 OE2 C:GLU180 3.7 33.3 1.0 CA B:CA201 3.9 34.5 1.0 CB C:GLU180 4.1 21.3 1.0 CG C:GLU180 4.4 19.4 1.0 O B:GLU180 4.5 23.4 1.0 CG B:GLU184 4.7 24.8 1.0

Calcium binding site 10 out of 13 in the Crystal Structure of Enterobacter Cloacae Ycdy, A Member of the Redox Enzyme Maturation Protein Family


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 10 of Crystal Structure of Enterobacter Cloacae Ycdy, A Member of the Redox Enzyme Maturation Protein Family within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca201 b:53.2 occ:1.00 OE1 B:GLU177 2.2 53.3 1.0 OE1 B:GLU180 2.6 32.7 1.0 OE2 C:GLU177 2.7 30.6 1.0 OE1 C:GLU177 2.8 27.8 1.0 OE2 C:GLU181 2.8 20.6 1.0 CD C:GLU177 3.1 24.6 1.0 CD B:GLU177 3.2 39.5 1.0 OE2 C:GLU180 3.3 33.3 1.0 CD C:GLU180 3.3 23.5 1.0 CD B:GLU180 3.5 31.2 1.0 OE1 C:GLU180 3.6 26.0 1.0 CG C:GLU180 3.8 19.4 1.0 CB B:GLU180 3.8 26.5 1.0 CD C:GLU181 3.8 20.8 1.0 O C:HOH303 3.9 3.6 1.0 OE2 B:GLU177 3.9 36.2 1.0 CA B:CA203 4.0 20.0 1.0 OE2 B:GLU181 4.1 19.3 1.0 CG B:GLU177 4.2 30.5 1.0 CG B:GLU180 4.2 32.0 1.0 OE2 B:GLU180 4.4 35.2 1.0 CE B:LYS-2 4.5 28.0 1.0 OE1 C:GLU181 4.6 25.4 1.0 CA B:CA201 4.6 34.5 1.0 CG C:GLU177 4.6 19.7 1.0 CG C:GLU181 4.7 18.0 1.0 O B:GLU177 4.7 16.3 1.0 CA B:GLU177 4.8 17.5 1.0 CD B:LYS-2 4.9 27.2 1.0

H.J.Choi, S.J.Lee, J.H.Kim, Y.B.You, S.I.Yoon. Structural Analysis of Ycdy, A Member of the Redox-Enzyme Maturation Protein Family. Acta Crystallogr.,Sect.F V. 81 263 2025.
ISSN: ESSN 2053-230X
PubMed: 40384351
DOI: 10.1107/S2053230X25003887