Zinc in PDB 8h4x: Structure of Cleaved Serpin B9

The structure of Structure of Cleaved Serpin B9, PDB code: 8h4x 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 (%)	17.1 / 19.9

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 19;

Binding sites:

The binding sites of Zinc atom in the Structure of Cleaved Serpin B9 (pdb code 8h4x). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 19 binding sites of Zinc where determined in the Structure of Cleaved Serpin B9, PDB code: 8h4x:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 19 in the Structure of Cleaved Serpin B9


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of Cleaved Serpin B9 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn401 b:99.9 occ:1.00 OE2 A:GLU141 2.6 52.9 1.0 OE1 A:GLU141 2.6 47.6 1.0 CD A:GLU141 3.0 44.1 1.0 O A:HOH518 3.0 47.7 1.0 HH22 A:ARG87 4.2 69.5 1.0 HA A:GLU141 4.2 35.1 1.0 HH12 A:ARG87 4.5 87.8 1.0 CG A:GLU141 4.5 37.4 1.0 O A:HOH626 4.8 66.3 1.0 HG2 A:GLU141 4.9 44.9 1.0 NH2 A:ARG87 4.9 57.9 1.0 HG3 A:GLU141 4.9 44.9 1.0 O A:LYS138 5.0 31.1 1.0

Zinc binding site 2 out of 19 in the Structure of Cleaved Serpin B9


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of Cleaved Serpin B9 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn402 b:94.5 occ:1.00 NE2 A:HIS286 2.0 37.6 0.5 OD1 A:ASP22 2.7 50.0 1.0 CD2 A:HIS286 3.0 35.1 0.5 OD2 A:ASP22 3.0 52.1 1.0 CE1 A:HIS286 3.1 45.1 0.5 HD2 A:HIS286 3.1 42.1 0.5 CG A:ASP22 3.2 53.9 1.0 HE1 A:HIS286 3.3 54.1 0.5 CG A:HIS286 4.1 48.8 0.5 ND1 A:HIS286 4.1 47.0 0.5 HG23 A:ILE18 4.3 36.3 1.0 HB2 A:SER282 4.6 48.3 1.0 HB2 A:HIS286 4.6 46.6 0.5 HG A:SER282 4.7 65.0 1.0 CB A:ASP22 4.7 36.9 1.0 OG A:SER282 4.9 54.1 1.0 HA A:ASP22 4.9 42.8 1.0 HD1 A:HIS286 4.9 56.3 0.5 HB3 A:ASP22 5.0 44.2 1.0

Zinc binding site 3 out of 19 in the Structure of Cleaved Serpin B9


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structure of Cleaved Serpin B9 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn403 b:41.6 occ:1.00 OD2 A:ASP258 2.0 38.2 1.0 O A:HOH521 2.1 36.4 1.0 SG A:CYS259 2.3 41.1 1.0 CG A:ASP258 2.9 39.8 1.0 OD1 A:ASP258 3.2 42.4 1.0 CB A:CYS259 3.6 34.3 1.0 ZN A:ZN405 3.7 49.4 1.0 HB2 A:CYS259 3.7 41.2 1.0 H A:CYS259 3.8 43.2 1.0 N A:CYS259 3.9 36.0 1.0 HA A:CYS259 4.0 41.5 1.0 CA A:CYS259 4.1 34.6 1.0 O A:ALA253 4.2 35.4 1.0 CB A:ASP258 4.3 39.5 1.0 C A:ASP258 4.3 40.5 1.0 HB3 A:CYS259 4.4 41.2 1.0 HB2 A:LYS256 4.4 48.2 1.0 HB2 A:ASP258 4.4 47.5 1.0 HB1 A:ALA253 4.7 42.4 1.0 O A:ASP258 4.7 42.8 1.0 HA A:TRP254 4.8 35.0 1.0 CA A:ASP258 4.9 38.9 1.0 HB3 A:ASP258 4.9 47.5 1.0

Zinc binding site 4 out of 19 in the Structure of Cleaved Serpin B9


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Structure of Cleaved Serpin B9 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn404 b:64.1 occ:1.00 NE2 A:HIS208 2.0 79.3 1.0 OD2 A:ASP234 2.1 47.0 1.0 O A:HOH618 2.6 61.2 1.0 CG A:ASP234 2.8 42.6 1.0 CD2 A:HIS208 2.9 43.0 1.0 HD2 A:HIS208 3.0 51.7 1.0 CE1 A:HIS208 3.1 73.7 1.0 OD1 A:ASP234 3.1 38.8 1.0 HE1 A:HIS208 3.3 88.4 1.0 HH21 A:ARG213 3.4 76.5 1.0 HE A:ARG213 4.1 100.6 1.0 CG A:HIS208 4.1 53.9 1.0 ND1 A:HIS208 4.1 65.8 1.0 CB A:ASP234 4.2 40.8 1.0 HA A:ARG213 4.2 43.3 1.0 NH2 A:ARG213 4.2 63.8 1.0 HB3 A:ASP234 4.3 48.9 1.0 HB2 A:ASP234 4.5 48.9 1.0 HG3 A:GLN215 4.7 37.4 1.0 HH22 A:ARG213 4.7 76.5 1.0 NE A:ARG213 4.8 83.8 1.0 HB3 A:ARG213 4.8 49.4 1.0 C A:ARG213 4.9 38.9 1.0 HD1 A:HIS208 4.9 79.0 1.0 CA A:ARG213 4.9 36.1 1.0 CZ A:ARG213 5.0 83.2 1.0

Zinc binding site 5 out of 19 in the Structure of Cleaved Serpin B9


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Structure of Cleaved Serpin B9 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn405 b:49.4 occ:1.00 SG A:CYS259 2.3 41.1 1.0 O A:HOH522 2.4 50.1 1.0 HA A:CYS259 2.9 41.5 1.0 CB A:CYS259 3.2 34.3 1.0 HB3 A:CYS259 3.3 41.2 1.0 CA A:CYS259 3.5 34.6 1.0 ZN A:ZN403 3.7 41.6 1.0 O A:HIS208 4.1 45.8 1.0 HB2 A:CYS259 4.1 41.2 1.0 N A:CYS259 4.4 36.0 1.0 O A:HOH588 4.5 40.5 1.0 HA A:VAL209 4.6 48.4 1.0 C A:CYS259 4.6 37.5 1.0 O A:ASP258 4.6 42.8 1.0 OD2 A:ASP258 4.6 38.2 1.0 HB1 A:ALA207 4.6 42.7 1.0 O A:CYS259 4.7 41.1 1.0 C A:ASP258 4.9 40.5 1.0 H A:CYS259 4.9 43.2 1.0 HA A:TRP254 5.0 35.0 1.0

Zinc binding site 6 out of 19 in the Structure of Cleaved Serpin B9


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Structure of Cleaved Serpin B9 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn406 b:69.1 occ:1.00 SG A:CYS98 2.3 56.9 1.0 OE2 A:GLU306 2.3 74.5 1.0 CD A:GLU306 3.1 77.6 1.0 HA A:CYS98 3.1 43.8 1.0 OE1 A:GLU306 3.3 55.8 1.0 CB A:CYS98 3.4 40.5 1.0 HB3 A:CYS98 3.7 48.6 1.0 CA A:CYS98 3.7 36.5 1.0 O A:THR97 3.9 42.4 1.0 HE A:ARG158 4.0 39.5 1.0 HD2 A:ARG158 4.0 39.0 1.0 N A:CYS98 4.2 35.4 1.0 HB2 A:CYS98 4.3 48.6 1.0 C A:THR97 4.3 39.8 1.0 CG A:GLU306 4.4 72.2 1.0 NE A:ARG158 4.5 33.0 1.0 HG2 A:GLU306 4.6 86.6 1.0 HG2 A:GLU95 4.6 41.2 1.0 HG3 A:GLU306 4.7 86.6 1.0 H A:CYS98 4.7 42.4 1.0 OG1 A:THR97 4.7 45.3 1.0 CD A:ARG158 4.8 32.5 1.0 HG3 A:GLU95 4.8 41.2 1.0 H A:GLN99 4.8 49.4 1.0 HD11 A:ILE122 5.0 41.1 1.0

Zinc binding site 7 out of 19 in the Structure of Cleaved Serpin B9


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Structure of Cleaved Serpin B9 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn407 b:99.2 occ:1.00 OE1 A:GLU177 2.5 115.8 1.0 OE2 A:GLU177 2.8 109.5 1.0 CD A:GLU177 2.9 105.8 1.0 OE1 A:GLU325 3.9 61.0 1.0 OE1 A:GLU324 4.0 34.7 1.0 HZ2 A:LYS271 4.1 83.3 1.0 HZ1 A:LYS271 4.2 83.3 1.0 CG A:GLU177 4.3 65.6 1.0 CD A:GLU325 4.5 90.8 1.0 OE2 A:GLU325 4.5 117.8 1.0 HG3 A:GLU177 4.5 78.8 1.0 NZ A:LYS271 4.6 69.4 1.0 HB2 A:GLU177 4.6 37.3 1.0 HB2 A:GLU324 4.8 32.9 1.0 CD A:GLU324 4.8 31.5 1.0 HB2 A:ASN323 4.9 30.6 1.0 HG2 A:GLU177 4.9 78.8 1.0

Zinc binding site 8 out of 19 in the Structure of Cleaved Serpin B9


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Structure of Cleaved Serpin B9 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn408 b:48.0 occ:1.00 O A:HOH609 2.0 47.1 1.0 OE1 A:GLU264 2.0 57.0 1.0 O A:HOH617 2.4 59.8 1.0 CD A:GLU264 2.7 70.4 1.0 OE2 A:GLU264 2.9 75.5 1.0 CG A:GLU264 4.2 59.3 1.0 HB2 A:GLU264 4.4 50.8 1.0 HG2 A:GLU264 4.5 71.2 1.0 CB A:GLU264 4.8 42.3 1.0 HG3 A:GLU264 4.8 71.2 1.0 HB3 A:GLU264 4.9 50.8 1.0

Zinc binding site 9 out of 19 in the Structure of Cleaved Serpin B9


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Structure of Cleaved Serpin B9 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn409 b:74.7 occ:1.00 O A:THR180 4.0 33.7 1.0 O A:THR178 4.1 33.0 1.0 O A:HOH562 4.2 43.3 1.0 HA A:THR178 4.3 41.9 1.0 O A:GLU177 4.5 31.2 1.0 C A:THR178 4.8 32.4 1.0 CA A:THR178 5.0 34.9 1.0

Zinc binding site 10 out of 19 in the Structure of Cleaved Serpin B9


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of Structure of Cleaved Serpin B9 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn410 b:94.3 occ:1.00 NE2 A:HIS286 2.0 54.9 0.5 CD2 A:HIS286 2.6 32.2 0.5 HD2 A:HIS286 2.6 38.6 0.5 CE1 A:HIS286 3.2 44.6 0.5 O A:HOH600 3.6 62.1 1.0 HE1 A:HIS286 3.6 53.5 0.5 CG A:HIS286 3.8 39.0 0.5 HD1 A:HIS286 3.9 56.3 0.5 ND1 A:HIS286 4.0 52.8 0.5 HG12 A:ILE18 4.3 35.8 1.0 ND1 A:HIS286 4.3 47.0 0.5 HB3 A:HIS286 4.6 46.1 0.5 HG13 A:ILE18 4.8 35.8 1.0 HD11 A:ILE18 4.8 37.9 1.0 CE1 A:HIS286 4.8 45.1 0.5 HE1 A:HIS286 4.8 54.1 0.5 HD1 A:HIS286 4.9 63.4 0.5 CG1 A:ILE18 4.9 29.8 1.0

A.Zhou, T.Yan. Expression, Purification and Crystallization of Cleaved Serpin B9 To Be Published.