Zinc in PDB 9le4: Crystal Structure of the Mit-Cd Complex of Stambp

The structure of Crystal Structure of the Mit-Cd Complex of Stambp, PDB code: 9le4 was solved by Z.Chen, J.Ding, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	22.43 / 2.60
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	58.349, 110.55, 270.458, 90, 90, 90
R / Rfree (%)	21.8 / 24.1

The binding sites of Zinc atom in the Crystal Structure of the Mit-Cd Complex of Stambp (pdb code 9le4). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the Crystal Structure of the Mit-Cd Complex of Stambp, PDB code: 9le4:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in the Crystal Structure of the Mit-Cd Complex of Stambp


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 the Mit-Cd Complex of Stambp within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn503 b:34.6 occ:1.00 OD2 B:ASP348 1.5 47.0 1.0 NE2 B:HIS337 1.8 33.7 1.0 NE2 B:HIS335 2.1 35.4 1.0 O B:HOH616 2.2 32.5 1.0 CG B:ASP348 2.7 46.3 1.0 CE1 B:HIS337 2.7 28.6 1.0 CD2 B:HIS337 2.8 36.4 1.0 CE1 B:HIS335 2.9 27.3 1.0 CD2 B:HIS335 3.1 29.1 1.0 OD1 B:ASP348 3.3 33.0 1.0 ND1 B:HIS337 3.8 34.4 1.0 CG B:HIS337 3.9 35.1 1.0 CB B:ASP348 3.9 42.1 1.0 ND1 B:HIS335 4.1 33.2 1.0 CG B:HIS335 4.2 33.1 1.0 OE2 B:GLU280 4.3 57.0 1.0 O B:PHE343 4.4 40.0 1.0 OG B:SER345 4.4 46.7 1.0 CB B:SER345 4.5 37.1 1.0 N B:SER345 4.6 38.4 1.0 OE1 B:GLU280 4.8 54.1 1.0 CD B:GLU280 4.9 57.0 1.0

Zinc binding site 2 out of 8 in the Crystal Structure of the Mit-Cd Complex of Stambp


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 the Mit-Cd Complex of Stambp within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn504 b:39.6 occ:1.00 NE2 B:HIS396 1.8 54.8 1.0 NE2 B:HIS398 2.0 45.0 1.0 NE2 B:HIS350 2.1 50.2 1.0 SG B:CYS390 2.3 52.2 1.0 CE1 B:HIS396 2.6 55.7 1.0 CE1 B:HIS350 2.8 44.0 1.0 CE1 B:HIS398 2.9 42.4 1.0 CD2 B:HIS396 3.0 55.3 1.0 CD2 B:HIS398 3.1 42.6 1.0 CB B:CYS390 3.2 43.5 1.0 CD2 B:HIS350 3.3 46.9 1.0 ND1 B:HIS396 3.8 60.3 1.0 CG B:HIS396 4.0 61.9 1.0 ND1 B:HIS350 4.0 38.2 1.0 ND1 B:HIS398 4.1 49.5 1.0 CG B:HIS398 4.1 47.2 1.0 CG B:HIS350 4.3 42.7 1.0 O B:GLN392 4.4 66.0 1.0 CA B:CYS390 4.6 48.4 1.0 CD1 B:ILE387 4.8 28.5 1.0 OG B:SER346 4.8 54.7 1.0 CB B:GLN392 4.8 59.7 1.0

Zinc binding site 3 out of 8 in the Crystal Structure of the Mit-Cd Complex of Stambp


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 the Mit-Cd Complex of Stambp within 5.0Å range: probe atom residue distance (Å) B Occ F:Zn503 b:47.6 occ:1.00 OD2 F:ASP348 1.5 44.2 1.0 NE2 F:HIS337 1.6 42.0 1.0 NE2 F:HIS335 2.1 51.8 1.0 O F:HOH615 2.2 64.8 1.0 CE1 F:HIS337 2.6 48.8 1.0 CG F:ASP348 2.6 45.1 1.0 CD2 F:HIS337 2.7 47.3 1.0 CD2 F:HIS335 3.0 42.4 1.0 CE1 F:HIS335 3.1 49.7 1.0 OD1 F:ASP348 3.2 46.1 1.0 ND1 F:HIS337 3.7 44.7 1.0 CG F:HIS337 3.8 44.7 1.0 CB F:ASP348 3.9 47.7 1.0 CG F:HIS335 4.1 44.7 1.0 ND1 F:HIS335 4.2 47.4 1.0 OE2 F:GLU280 4.3 61.2 1.0 OG F:SER345 4.4 51.8 1.0 O F:PHE343 4.6 49.0 1.0 CB F:SER345 4.6 53.4 1.0 OE1 F:GLU280 4.7 72.1 1.0 N F:SER345 4.7 55.0 1.0 CD F:GLU280 4.8 69.7 1.0 CG1 F:VAL366 5.0 47.4 1.0

Zinc binding site 4 out of 8 in the Crystal Structure of the Mit-Cd Complex of Stambp


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 the Mit-Cd Complex of Stambp within 5.0Å range: probe atom residue distance (Å) B Occ F:Zn504 b:127.1 occ:1.00 NE2 F:HIS398 1.7 68.0 1.0 NE2 F:HIS396 1.9 88.9 1.0 NE2 F:HIS350 2.0 84.9 1.0 SG F:CYS390 2.3 84.6 1.0 CE1 F:HIS398 2.7 80.0 1.0 CE1 F:HIS350 2.7 80.5 1.0 CD2 F:HIS396 2.8 81.7 1.0 CD2 F:HIS398 2.8 79.2 1.0 CE1 F:HIS396 2.9 89.3 1.0 CB F:CYS390 3.0 80.7 1.0 CD2 F:HIS350 3.2 74.8 1.0 ND1 F:HIS398 3.8 79.0 1.0 CG F:HIS398 3.9 71.8 1.0 ND1 F:HIS350 3.9 75.8 1.0 CG F:HIS396 3.9 81.3 1.0 ND1 F:HIS396 4.0 85.3 1.0 CG F:HIS350 4.1 68.2 1.0 O F:GLN392 4.2 94.1 1.0 CA F:CYS390 4.5 81.5 1.0 C F:CYS390 4.8 83.4 1.0 CB F:GLN392 4.9 84.5 1.0

Zinc binding site 5 out of 8 in the Crystal Structure of the Mit-Cd Complex of Stambp


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 the Mit-Cd Complex of Stambp within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn501 b:47.6 occ:1.00 OD2 D:ASP348 1.4 39.1 1.0 NE2 D:HIS335 2.0 38.6 1.0 NE2 D:HIS337 2.2 45.9 1.0 O D:HOH624 2.4 54.9 1.0 CG D:ASP348 2.5 50.0 1.0 CE1 D:HIS335 2.8 37.2 1.0 OD1 D:ASP348 3.1 59.6 1.0 CD2 D:HIS335 3.1 36.9 1.0 CD2 D:HIS337 3.2 47.6 1.0 CE1 D:HIS337 3.2 46.4 1.0 CB D:ASP348 3.8 50.9 1.0 ND1 D:HIS335 3.9 33.7 1.0 CG D:HIS335 4.1 34.0 1.0 OG D:SER345 4.1 43.4 1.0 ND1 D:HIS337 4.3 47.3 1.0 CG D:HIS337 4.3 47.8 1.0 O D:PHE343 4.4 40.9 1.0 OE2 D:GLU280 4.5 65.1 1.0 N D:SER345 4.7 42.5 1.0 CB D:SER345 4.7 40.3 1.0 OE1 D:GLU280 4.8 56.6 1.0

Zinc binding site 6 out of 8 in the Crystal Structure of the Mit-Cd Complex of Stambp


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 the Mit-Cd Complex of Stambp within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn502 b:56.4 occ:1.00 NE2 D:HIS396 1.6 61.8 1.0 NE2 D:HIS398 2.0 51.9 1.0 NE2 D:HIS350 2.3 54.6 1.0 SG D:CYS390 2.3 65.3 1.0 CE1 D:HIS396 2.5 70.0 1.0 CD2 D:HIS396 2.6 68.1 1.0 CE1 D:HIS398 2.9 52.7 1.0 CD2 D:HIS398 3.0 52.8 1.0 CE1 D:HIS350 3.1 51.4 1.0 CB D:CYS390 3.3 58.1 1.0 CD2 D:HIS350 3.3 58.8 1.0 ND1 D:HIS396 3.6 71.6 1.0 CG D:HIS396 3.7 70.0 1.0 ND1 D:HIS398 4.1 51.3 1.0 CG D:HIS398 4.1 58.8 1.0 ND1 D:HIS350 4.3 48.4 1.0 O D:GLN392 4.4 79.4 1.0 CG D:HIS350 4.4 51.2 1.0 CD1 D:ILE387 4.7 49.6 1.0 CA D:CYS390 4.7 60.0 1.0 CB D:GLN392 4.9 68.9 1.0

Zinc binding site 7 out of 8 in the Crystal Structure of the Mit-Cd Complex of Stambp


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 the Mit-Cd Complex of Stambp within 5.0Å range: probe atom residue distance (Å) B Occ H:Zn501 b:47.3 occ:1.00 OD2 H:ASP348 1.6 57.6 1.0 NE2 H:HIS337 1.8 54.0 1.0 NE2 H:HIS335 2.0 51.0 1.0 O H:HOH604 2.1 51.7 1.0 CE1 H:HIS337 2.7 52.6 1.0 CG H:ASP348 2.7 45.3 1.0 CD2 H:HIS337 2.9 53.1 1.0 CE1 H:HIS335 3.0 45.4 1.0 CD2 H:HIS335 3.0 47.9 1.0 OD1 H:ASP348 3.3 50.5 1.0 ND1 H:HIS337 3.8 52.4 1.0 CG H:HIS337 3.9 58.1 1.0 CB H:ASP348 4.0 45.8 1.0 ND1 H:HIS335 4.1 41.8 1.0 CG H:HIS335 4.1 43.6 1.0 OE2 H:GLU280 4.2 70.4 1.0 OG H:SER345 4.3 44.0 1.0 O H:PHE343 4.4 50.1 1.0 OE1 H:GLU280 4.6 62.5 1.0 CB H:SER345 4.7 45.9 1.0 N H:SER345 4.7 51.2 1.0 CD H:GLU280 4.8 71.6 1.0 CG1 H:VAL366 4.9 49.1 1.0

Zinc binding site 8 out of 8 in the Crystal Structure of the Mit-Cd Complex of Stambp


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 the Mit-Cd Complex of Stambp within 5.0Å range: probe atom residue distance (Å) B Occ H:Zn502 b:57.8 occ:1.00 NE2 H:HIS396 1.5 62.5 1.0 NE2 H:HIS350 2.1 57.7 1.0 NE2 H:HIS398 2.1 54.8 1.0 SG H:CYS390 2.3 71.3 1.0 CE1 H:HIS396 2.4 67.8 1.0 CD2 H:HIS396 2.7 65.3 1.0 CE1 H:HIS350 2.9 50.0 1.0 CD2 H:HIS398 3.1 57.8 1.0 CE1 H:HIS398 3.1 59.7 1.0 CD2 H:HIS350 3.1 54.2 1.0 CB H:CYS390 3.3 55.9 1.0 ND1 H:HIS396 3.5 69.9 1.0 CG H:HIS396 3.7 68.9 1.0 ND1 H:HIS350 4.1 48.6 1.0 ND1 H:HIS398 4.2 67.8 1.0 CG H:HIS350 4.2 44.9 1.0 CG H:HIS398 4.2 63.4 1.0 CD1 H:ILE387 4.5 46.1 1.0 NE2 H:GLN392 4.5 76.9 1.0 OG H:SER346 4.7 73.1 1.0 CA H:CYS390 4.7 64.5 1.0 CB H:GLN392 4.8 79.7 1.0 CD H:GLN392 4.9 80.8 1.0 O H:GLN392 5.0 85.0 1.0

Z.Chen, G.Wang, Y.Zhang, J.Ding. The Mit Domain of Stambp Autoinhibits Its Deubiquitination Activity. Structure 2025.
ISSN: ISSN 0969-2126
PubMed: 40441142
DOI: 10.1016/J.STR.2025.05.001