Zinc in PDB 8zcr: Structure of PI9

The structure of Structure of PI9, PDB code: 8zcr was solved by A.Zhou, T.Yan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	52.66 / 1.93
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	68.512, 82.323, 101.167, 90, 90, 90
R / Rfree (%)	18 / 20.9

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 18;

Binding sites:

The binding sites of Zinc atom in the Structure of PI9 (pdb code 8zcr). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 18 binding sites of Zinc where determined in the Structure of PI9, PDB code: 8zcr:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 18 in the Structure of PI9


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of PI9 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn401 b:98.9 occ:1.00 OE2 A:GLU141 2.6 56.3 1.0 OE1 A:GLU141 2.7 48.9 1.0 O A:HOH552 2.9 48.2 1.0 CD A:GLU141 3.0 49.3 1.0 HH22 A:ARG87 4.1 60.6 1.0 HA A:GLU141 4.3 38.1 1.0 HH12 A:ARG87 4.4 79.3 1.0 CG A:GLU141 4.5 35.6 1.0 O A:HOH631 4.8 60.7 1.0 NH2 A:ARG87 4.9 50.5 1.0 HG2 A:GLU141 4.9 42.7 1.0 HG3 A:GLU141 4.9 42.7 1.0

Zinc binding site 2 out of 18 in the Structure of PI9


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of PI9 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn402 b:90.1 occ:1.00 NE2 A:HIS286 2.1 35.7 0.5 OD1 A:ASP22 2.7 49.9 1.0 OD2 A:ASP22 2.9 55.1 1.0 CD2 A:HIS286 3.0 38.2 0.5 HD2 A:HIS286 3.1 45.8 0.5 CE1 A:HIS286 3.1 41.2 0.5 CG A:ASP22 3.2 48.1 1.0 HE1 A:HIS286 3.4 49.5 0.5 CG A:HIS286 4.1 43.7 0.5 ND1 A:HIS286 4.2 44.4 0.5 HG23 A:ILE18 4.3 32.0 1.0 HB2 A:SER282 4.5 45.9 1.0 HB2 A:HIS286 4.6 46.4 0.5 CB A:ASP22 4.7 35.6 1.0 HG A:SER282 4.7 60.2 1.0 OG A:SER282 4.9 50.2 1.0 HA A:ASP22 4.9 35.9 1.0 HB3 A:ASP22 5.0 42.8 1.0 HD1 A:HIS286 5.0 53.3 0.5

Zinc binding site 3 out of 18 in the Structure of PI9


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structure of PI9 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn403 b:36.7 occ:1.00 OD2 A:ASP258 1.9 33.7 1.0 O A:HOH531 2.3 33.8 1.0 SG A:CYS259 2.4 35.9 1.0 CG A:ASP258 2.9 35.0 1.0 OD1 A:ASP258 3.2 39.0 1.0 CB A:CYS259 3.6 31.0 1.0 ZN A:ZN405 3.7 45.4 1.0 HB2 A:CYS259 3.7 37.2 1.0 N A:CYS259 3.9 32.1 1.0 H A:CYS259 4.0 38.6 1.0 HA A:CYS259 4.0 37.7 1.0 CA A:CYS259 4.1 31.4 1.0 CB A:ASP258 4.2 35.2 1.0 C A:ASP258 4.3 39.1 1.0 HB2 A:ASP258 4.3 42.2 1.0 O A:ALA253 4.3 32.8 1.0 HB2 A:LYS256 4.4 49.1 1.0 HB3 A:CYS259 4.4 37.2 1.0 HB1 A:ALA253 4.7 37.9 1.0 O A:ASP258 4.7 33.8 1.0 CA A:ASP258 4.8 34.5 1.0 HB3 A:ASP258 4.9 42.2 1.0 HA A:TRP254 4.9 32.0 1.0

Zinc binding site 4 out of 18 in the Structure of PI9


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Structure of PI9 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn404 b:59.6 occ:1.00 NE2 A:HIS208 2.0 70.0 1.0 OD2 A:ASP234 2.1 49.6 1.0 O A:HOH623 2.8 57.1 1.0 CG A:ASP234 2.8 41.7 1.0 CD2 A:HIS208 2.9 39.8 1.0 CE1 A:HIS208 3.0 64.5 1.0 OD1 A:ASP234 3.0 38.7 1.0 HD2 A:HIS208 3.0 47.8 1.0 HE1 A:HIS208 3.3 77.5 1.0 HH21 A:ARG213 3.3 70.8 1.0 HE A:ARG213 3.9 83.2 1.0 CG A:HIS208 4.1 48.1 1.0 ND1 A:HIS208 4.1 57.0 1.0 NH2 A:ARG213 4.1 58.9 1.0 CB A:ASP234 4.2 44.6 1.0 HA A:ARG213 4.2 44.4 1.0 HB3 A:ASP234 4.3 53.5 1.0 HB2 A:ASP234 4.5 53.5 1.0 NE A:ARG213 4.6 69.3 1.0 HH22 A:ARG213 4.6 70.8 1.0 HG3 A:GLN215 4.7 36.4 1.0 HB3 A:ARG213 4.8 51.2 1.0 C A:ARG213 4.9 37.1 1.0 CZ A:ARG213 4.9 68.7 1.0 HD1 A:HIS208 4.9 68.4 1.0 CA A:ARG213 4.9 37.0 1.0 N A:ALA214 5.0 34.7 1.0

Zinc binding site 5 out of 18 in the Structure of PI9


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Structure of PI9 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn405 b:45.4 occ:1.00 SG A:CYS259 2.4 35.9 1.0 O A:HOH629 2.5 48.7 1.0 HA A:CYS259 2.8 37.7 1.0 CB A:CYS259 3.3 31.0 1.0 HB3 A:CYS259 3.5 37.2 1.0 CA A:CYS259 3.5 31.4 1.0 ZN A:ZN403 3.7 36.7 1.0 O A:HIS208 4.0 43.4 1.0 HB2 A:CYS259 4.2 37.2 1.0 N A:CYS259 4.5 32.1 1.0 O A:HOH590 4.5 37.7 1.0 HA A:VAL209 4.5 44.9 1.0 C A:CYS259 4.6 34.0 1.0 OD2 A:ASP258 4.6 33.7 1.0 O A:CYS259 4.6 37.1 1.0 O A:ASP258 4.6 33.8 1.0 HB1 A:ALA207 4.7 37.3 1.0 C A:ASP258 4.9 39.1 1.0 HA A:TRP254 5.0 32.0 1.0

Zinc binding site 6 out of 18 in the Structure of PI9


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Structure of PI9 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn406 b:65.4 occ:1.00 OE2 A:GLU306 1.8 67.1 1.0 SG A:CYS98 2.2 54.0 1.0 CD A:GLU306 2.6 66.3 1.0 OE1 A:GLU306 2.8 56.1 1.0 HA A:CYS98 3.2 45.0 1.0 CB A:CYS98 3.4 43.4 1.0 HB3 A:CYS98 3.4 52.1 1.0 CA A:CYS98 3.8 37.5 1.0 HD2 A:ARG158 3.9 44.8 1.0 HE A:ARG158 3.9 40.4 1.0 CG A:GLU306 3.9 71.3 1.0 HG2 A:GLU306 4.1 85.6 1.0 HG3 A:GLU306 4.2 85.6 1.0 HB2 A:CYS98 4.2 52.1 1.0 O A:THR97 4.2 45.8 1.0 N A:CYS98 4.4 37.2 1.0 NE A:ARG158 4.5 33.7 1.0 H A:GLN99 4.6 45.4 1.0 CD A:ARG158 4.6 37.3 1.0 C A:THR97 4.6 43.7 1.0 HG2 A:GLU95 4.9 41.3 1.0 H A:CYS98 5.0 44.6 1.0

Zinc binding site 7 out of 18 in the Structure of PI9


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Structure of PI9 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn407 b:42.2 occ:1.00 O A:HOH611 2.0 48.8 1.0 OE1 A:GLU264 2.1 59.9 1.0 CD A:GLU264 2.8 57.1 1.0 OE2 A:GLU264 2.8 59.5 1.0 CG A:GLU264 4.2 52.1 1.0 HB2 A:GLU264 4.4 51.0 1.0 HG2 A:GLU264 4.5 62.6 1.0 HG3 A:GLU264 4.8 62.6 1.0 CB A:GLU264 4.8 42.5 1.0 HB3 A:GLU264 4.9 51.0 1.0

Zinc binding site 8 out of 18 in the Structure of PI9


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Structure of PI9 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn408 b:88.5 occ:1.00 NE2 A:HIS286 2.0 49.6 0.5 CD2 A:HIS286 2.7 39.6 0.5 HD2 A:HIS286 2.7 47.5 0.5 CE1 A:HIS286 3.1 45.3 0.5 HE1 A:HIS286 3.5 54.4 0.5 O A:HOH610 3.6 58.3 1.0 HD1 A:HIS286 3.9 53.3 0.5 CG A:HIS286 3.9 42.7 0.5 ND1 A:HIS286 4.1 46.6 0.5 HG12 A:ILE18 4.3 38.2 1.0 ND1 A:HIS286 4.3 44.4 0.5 HB3 A:HIS286 4.7 45.4 0.5 HE1 A:HIS286 4.7 49.5 0.5 CE1 A:HIS286 4.8 41.2 0.5 HG13 A:ILE18 4.8 38.2 1.0 HD11 A:ILE18 4.8 40.0 1.0 HD1 A:HIS286 4.9 56.0 0.5 OE1 A:GLN21 4.9 67.3 1.0 CG1 A:ILE18 5.0 31.8 1.0

Zinc binding site 9 out of 18 in the Structure of PI9


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Structure of PI9 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn409 b:57.8 occ:1.00 OE2 A:GLU276 2.4 34.9 1.0 O A:HOH599 2.9 33.1 1.0 HE1 A:HIS26 3.0 45.8 1.0 OE1 A:GLU276 3.0 28.9 1.0 CD A:GLU276 3.0 35.1 1.0 HB2 A:ASN27 3.1 29.8 1.0 HD22 A:ASN27 3.3 35.4 1.0 CE1 A:HIS26 3.6 38.1 1.0 O A:GLN275 3.8 27.4 1.0 H A:GLN275 4.0 26.8 1.0 CB A:ASN27 4.0 24.8 1.0 HD22 A:LEU274 4.1 38.5 1.0 ND2 A:ASN27 4.1 29.4 1.0 NE2 A:HIS26 4.3 45.0 1.0 ND1 A:HIS26 4.3 36.2 1.0 HB3 A:ASN27 4.4 29.8 1.0 HD1 A:HIS26 4.4 43.5 1.0 CG A:GLU276 4.4 28.4 1.0 HG2 A:GLU276 4.5 34.2 1.0 HB3 A:LEU274 4.5 29.5 1.0 H A:ASN27 4.5 31.9 1.0 CG A:ASN27 4.6 26.5 1.0 HA A:LEU274 4.7 30.6 1.0 HD21 A:ASN27 4.7 35.4 1.0 HA A:GLU276 4.7 30.5 1.0 C A:GLN275 4.8 29.3 1.0 N A:GLN275 4.8 22.3 1.0 O A:ASN27 4.8 24.3 1.0 HD23 A:LEU274 4.9 38.5 1.0 HG3 A:GLU276 4.9 34.2 1.0 CD2 A:LEU274 4.9 32.0 1.0 CA A:ASN27 5.0 25.6 1.0

Zinc binding site 10 out of 18 in the Structure of PI9


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of Structure of PI9 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn410 b:70.7 occ:1.00 OE1 A:GLU118 2.4 45.7 1.0 O A:HOH505 2.5 42.7 1.0 OE2 A:GLU118 2.8 65.6 1.0 CD A:GLU118 2.9 49.4 1.0 CG A:GLU118 4.4 31.6 1.0 HB2 A:LYS96 4.6 43.5 1.0 O A:LYS96 4.7 38.3 1.0 HB2 A:GLU118 4.8 37.8 1.0 HG3 A:GLU118 4.8 38.0 1.0 HG2 A:GLU118 4.9 38.0 1.0 HE22 A:GLN99 4.9 88.2 1.0 HB3 A:GLU118 4.9 37.8 1.0 CB A:GLU118 5.0 31.4 1.0

T.Yan, A.Zhou. Crystallization and Crystallographic Studies of Human Serine Protease Inhibitor (Serpin) B9. Acta Crystallogr.,Sect.F V. 80 286 2024.
ISSN: ESSN 2053-230X
PubMed: 39382088
DOI: 10.1107/S2053230X24009439