Zinc in PDB 5up9: Crystal Structure of Zn-Bound Human Heavy-Chain Ferritin Variant 122H- Delta C-Star with Para-Xylenedihydroxamate

All present enzymatic activity of Crystal Structure of Zn-Bound Human Heavy-Chain Ferritin Variant 122H- Delta C-Star with Para-Xylenedihydroxamate:
1.16.3.1;

The structure of Crystal Structure of Zn-Bound Human Heavy-Chain Ferritin Variant 122H- Delta C-Star with Para-Xylenedihydroxamate, PDB code: 5up9 was solved by J.B.Bailey, L.Zhang, J.A.Chiong, S.Ahn, F.A.Tezcan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.40 / 2.45
Space group	I 4
Cell size a, b, c (Å), α, β, γ (°)	149.883, 149.883, 162.228, 90.00, 90.00, 90.00
R / Rfree (%)	24.1 / 28.9

Pages:

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

Binding sites:

The binding sites of Zinc atom in the Crystal Structure of Zn-Bound Human Heavy-Chain Ferritin Variant 122H- Delta C-Star with Para-Xylenedihydroxamate (pdb code 5up9). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 19 binding sites of Zinc where determined in the Crystal Structure of Zn-Bound Human Heavy-Chain Ferritin Variant 122H- Delta C-Star with Para-Xylenedihydroxamate, PDB code: 5up9:
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 Crystal Structure of Zn-Bound Human Heavy-Chain Ferritin Variant 122H- Delta C-Star with Para-Xylenedihydroxamate


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 Zn-Bound Human Heavy-Chain Ferritin Variant 122H- Delta C-Star with Para-Xylenedihydroxamate within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn201 b:25.4 occ:1.00 O A:HOH327 2.0 21.0 1.0 ND1 A:HIS65 2.1 22.9 1.0 O A:HOH322 2.1 23.3 1.0 OE2 A:GLU62 2.1 31.5 1.0 OE1 A:GLU27 2.2 32.9 1.0 CE1 A:HIS65 3.0 28.9 1.0 CD A:GLU27 3.1 22.8 1.0 CG A:HIS65 3.2 20.3 1.0 CD A:GLU62 3.2 22.7 1.0 ZN A:ZN202 3.3 31.8 1.0 OE2 A:GLU27 3.5 28.3 1.0 CB A:HIS65 3.6 24.8 1.0 OE1 A:GLU62 3.6 39.3 1.0 NE2 A:GLN141 3.7 33.7 1.0 O A:HOH392 4.1 30.2 1.0 NE2 A:HIS65 4.1 30.1 1.0 CG1 A:VAL110 4.2 19.9 1.0 CD2 A:HIS65 4.3 19.5 1.0 O A:HOH397 4.4 29.7 1.0 CG A:GLU27 4.4 12.3 1.0 CA A:GLU62 4.4 21.7 1.0 CG A:GLU62 4.5 20.9 1.0 CB A:GLU62 4.7 22.7 1.0 CB A:GLU27 4.7 14.5 1.0 CD A:GLN141 4.9 20.7 1.0 CA A:GLU27 5.0 22.3 1.0

Zinc binding site 2 out of 19 in the Crystal Structure of Zn-Bound Human Heavy-Chain Ferritin Variant 122H- Delta C-Star with Para-Xylenedihydroxamate


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 Zn-Bound Human Heavy-Chain Ferritin Variant 122H- Delta C-Star with Para-Xylenedihydroxamate within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn202 b:31.8 occ:1.00 OE1 A:GLU62 1.9 39.3 1.0 O A:HOH327 2.0 21.0 1.0 O A:HOH397 2.2 29.7 1.0 OE1 A:GLU107 2.3 24.2 1.0 OE2 A:GLU107 2.5 21.9 1.0 CD A:GLU107 2.7 22.5 1.0 CD A:GLU62 2.9 22.7 1.0 OE2 A:GLU62 3.1 31.5 1.0 ZN A:ZN201 3.3 25.4 1.0 O A:HOH405 4.1 40.9 1.0 NE2 A:GLN141 4.1 33.7 1.0 CE1 A:HIS65 4.1 28.9 1.0 CG A:GLU107 4.2 17.7 1.0 CG A:GLU62 4.3 20.9 1.0 CE2 A:TYR34 4.3 30.7 1.0 ND1 A:HIS65 4.3 22.9 1.0 OH A:TYR34 4.4 33.2 1.0 OE1 A:GLN141 4.4 31.5 1.0 O A:HOH322 4.6 23.3 1.0 CD A:GLN141 4.6 20.7 1.0 CZ A:TYR34 4.8 29.1 1.0

Zinc binding site 3 out of 19 in the Crystal Structure of Zn-Bound Human Heavy-Chain Ferritin Variant 122H- Delta C-Star with Para-Xylenedihydroxamate


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 Zn-Bound Human Heavy-Chain Ferritin Variant 122H- Delta C-Star with Para-Xylenedihydroxamate within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn203 b:54.7 occ:0.75 O A:HOH390 1.9 13.9 1.0 NE2 A:HIS173 2.1 38.5 1.0 NE2 E:HIS173 2.4 26.7 1.0 NE2 F:HIS173 2.5 32.7 1.0 CE1 E:HIS173 2.5 32.5 1.0 CE1 A:HIS173 2.6 41.1 1.0 CE1 D:HIS173 2.7 36.8 1.0 NE2 D:HIS173 2.8 41.3 1.0 CE1 F:HIS173 2.8 39.8 1.0 CD2 A:HIS173 3.4 29.7 1.0 CD2 F:HIS173 3.7 33.1 1.0 CD2 E:HIS173 3.7 34.2 1.0 ND1 E:HIS173 3.8 34.4 1.0 ND1 A:HIS173 3.8 34.5 1.0 O D:HOH441 4.0 29.5 1.0 ND1 D:HIS173 4.0 36.1 1.0 ND1 F:HIS173 4.0 38.5 1.0 CD2 D:HIS173 4.1 45.5 1.0 CG A:HIS173 4.2 33.8 1.0 CG E:HIS173 4.4 33.1 1.0 CG F:HIS173 4.5 33.9 1.0 CD2 A:LEU169 4.6 20.4 1.0 CG D:HIS173 4.7 39.3 1.0 CD2 E:LEU169 4.7 18.9 1.0 CD2 D:LEU169 4.8 21.8 1.0 CD2 F:LEU169 4.9 24.2 1.0

Zinc binding site 4 out of 19 in the Crystal Structure of Zn-Bound Human Heavy-Chain Ferritin Variant 122H- Delta C-Star with Para-Xylenedihydroxamate


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 Zn-Bound Human Heavy-Chain Ferritin Variant 122H- Delta C-Star with Para-Xylenedihydroxamate within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn204 b:62.7 occ:1.00 OE2 A:GLU134 2.5 29.5 1.0 OD1 A:ASP131 2.9 33.0 1.0 CD A:GLU134 3.7 29.4 1.0 CG A:ASP131 4.0 34.9 1.0 OE1 A:GLU134 4.4 35.2 1.0 O A:HOH330 4.4 32.0 1.0 CB A:ASP131 4.5 22.9 1.0 CB A:GLU134 4.6 18.1 1.0 CG A:GLU134 4.7 23.6 1.0 CA A:ASP131 4.8 22.5 1.0

Zinc binding site 5 out of 19 in the Crystal Structure of Zn-Bound Human Heavy-Chain Ferritin Variant 122H- Delta C-Star with Para-Xylenedihydroxamate


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 Zn-Bound Human Heavy-Chain Ferritin Variant 122H- Delta C-Star with Para-Xylenedihydroxamate within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn202 b:23.5 occ:1.00 ND1 B:HIS65 2.0 29.3 1.0 O B:HOH312 2.1 20.7 1.0 O B:HOH301 2.1 24.2 1.0 OE1 B:GLU27 2.2 23.2 1.0 OE2 B:GLU62 2.2 26.9 1.0 CE1 B:HIS65 2.8 26.0 1.0 CD B:GLU27 3.0 16.6 1.0 CG B:HIS65 3.1 23.1 1.0 ZN B:ZN203 3.2 28.3 1.0 OE2 B:GLU27 3.2 21.5 1.0 CD B:GLU62 3.3 21.3 1.0 CB B:HIS65 3.6 29.5 1.0 OE1 B:GLN141 3.6 28.1 1.0 OE1 B:GLU62 3.6 26.9 1.0 NE2 B:HIS65 4.0 28.0 1.0 CG1 B:VAL110 4.1 9.7 1.0 CD2 B:HIS65 4.1 20.0 1.0 O B:HOH398 4.4 26.1 1.0 CG B:GLU27 4.4 19.4 1.0 CA B:GLU62 4.5 19.8 1.0 CG B:GLU62 4.6 20.3 1.0 CD B:GLN141 4.8 17.1 1.0 CB B:GLU62 4.8 24.2 1.0 OE2 B:GLU107 4.9 23.8 1.0 CB B:GLU27 4.9 12.8 1.0

Zinc binding site 6 out of 19 in the Crystal Structure of Zn-Bound Human Heavy-Chain Ferritin Variant 122H- Delta C-Star with Para-Xylenedihydroxamate


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 Zn-Bound Human Heavy-Chain Ferritin Variant 122H- Delta C-Star with Para-Xylenedihydroxamate within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn203 b:28.3 occ:1.00 OE1 B:GLU62 1.9 26.9 1.0 O B:HOH398 2.0 26.1 1.0 O B:HOH301 2.0 24.2 1.0 OE1 B:GLU107 2.2 28.6 1.0 OE2 B:GLU107 2.4 23.8 1.0 CD B:GLU107 2.6 18.6 1.0 CD B:GLU62 2.8 21.3 1.0 OE2 B:GLU62 3.1 26.9 1.0 ZN B:ZN202 3.2 23.5 1.0 O B:HOH391 3.8 31.4 1.0 CE1 B:HIS65 3.9 26.0 1.0 OE1 B:GLN141 4.0 28.1 1.0 CG B:GLU107 4.1 19.4 1.0 ND1 B:HIS65 4.2 29.3 1.0 CG B:GLU62 4.2 20.3 1.0 CE2 B:TYR34 4.3 23.1 1.0 NE2 B:GLN141 4.5 15.1 1.0 OH B:TYR34 4.5 30.5 1.0 CD B:GLN141 4.6 17.1 1.0 O B:HOH312 4.7 20.7 1.0 CZ B:TYR34 4.9 21.3 1.0 CB B:GLU107 5.0 18.6 1.0

Zinc binding site 7 out of 19 in the Crystal Structure of Zn-Bound Human Heavy-Chain Ferritin Variant 122H- Delta C-Star with Para-Xylenedihydroxamate


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 Zn-Bound Human Heavy-Chain Ferritin Variant 122H- Delta C-Star with Para-Xylenedihydroxamate within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn204 b:43.8 occ:0.25 O B:HOH456 2.0 41.1 0.2 NE2 B:HIS173 2.6 38.2 1.0 CE1 B:HIS173 3.3 43.2 1.0 CD2 B:HIS173 3.7 34.2 1.0 CD2 B:LEU169 4.3 23.3 1.0 ND1 B:HIS173 4.5 40.0 1.0 CG B:HIS173 4.8 39.8 1.0

Zinc binding site 8 out of 19 in the Crystal Structure of Zn-Bound Human Heavy-Chain Ferritin Variant 122H- Delta C-Star with Para-Xylenedihydroxamate


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 Zn-Bound Human Heavy-Chain Ferritin Variant 122H- Delta C-Star with Para-Xylenedihydroxamate within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn205 b:23.1 occ:1.00 NE2 B:HIS122 2.1 32.3 1.0 O14 B:BYX207 2.2 35.8 1.0 O13 B:BYX207 2.2 30.9 1.0 NE2 F:HIS122 2.3 37.3 1.0 CE1 F:HIS122 2.4 23.1 1.0 CE1 B:HIS122 2.7 28.4 1.0 C11 B:BYX207 2.9 33.5 1.0 N12 B:BYX207 3.0 32.7 1.0 CD2 B:HIS122 3.3 23.2 1.0 O B:HOH404 3.5 37.5 1.0 ND1 F:HIS122 3.7 24.5 1.0 CD2 F:HIS122 3.7 34.7 1.0 H121 B:BYX207 3.8 39.2 1.0 ND1 B:HIS122 4.0 31.6 1.0 O B:HOH363 4.1 26.3 1.0 O F:HOH393 4.1 30.8 1.0 CG B:HIS122 4.3 37.4 1.0 CG F:HIS122 4.3 27.9 1.0 C10 B:BYX207 4.4 31.6 1.0 H081 B:BYX207 4.6 48.5 1.0 H101 B:BYX207 4.7 38.0 1.0 O F:HOH445 4.9 33.2 1.0 H102 B:BYX207 5.0 38.0 1.0 C08 B:BYX207 5.0 40.5 1.0 C09 B:BYX207 5.0 41.2 1.0

Zinc binding site 9 out of 19 in the Crystal Structure of Zn-Bound Human Heavy-Chain Ferritin Variant 122H- Delta C-Star with Para-Xylenedihydroxamate


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Crystal Structure of Zn-Bound Human Heavy-Chain Ferritin Variant 122H- Delta C-Star with Para-Xylenedihydroxamate within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn201 b:26.4 occ:1.00 NE2 C:HIS122 2.0 33.7 1.0 NE2 E:HIS122 2.1 34.7 1.0 CE1 E:HIS122 2.5 39.9 1.0 CE1 C:HIS122 2.8 28.6 1.0 CD2 C:HIS122 3.2 31.1 1.0 CD2 E:HIS122 3.4 30.7 1.0 ND1 E:HIS122 3.8 39.6 1.0 O E:HOH420 3.9 34.2 1.0 ND1 C:HIS122 4.0 33.7 1.0 CG E:HIS122 4.2 33.2 1.0 CG C:HIS122 4.2 38.9 1.0

Zinc binding site 10 out of 19 in the Crystal Structure of Zn-Bound Human Heavy-Chain Ferritin Variant 122H- Delta C-Star with Para-Xylenedihydroxamate


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of Crystal Structure of Zn-Bound Human Heavy-Chain Ferritin Variant 122H- Delta C-Star with Para-Xylenedihydroxamate within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn202 b:25.5 occ:1.00 ND1 C:HIS65 2.0 27.2 1.0 OE1 C:GLU27 2.1 21.8 1.0 O C:HOH309 2.3 21.4 1.0 OE2 C:GLU62 2.3 18.3 1.0 O C:HOH301 2.4 28.1 1.0 CE1 C:HIS65 2.9 30.0 1.0 CD C:GLU27 3.0 18.1 1.0 CG C:HIS65 3.1 24.1 1.0 ZN C:ZN203 3.1 29.7 1.0 OE2 C:GLU27 3.3 16.4 1.0 CD C:GLU62 3.3 17.4 1.0 CB C:HIS65 3.6 25.9 1.0 OE1 C:GLU62 3.6 20.5 1.0 OE1 C:GLN141 3.7 28.2 1.0 NE2 C:HIS65 4.1 25.0 1.0 CD2 C:HIS65 4.2 21.2 1.0 CG1 C:VAL110 4.2 16.0 1.0 CG C:GLU27 4.4 15.3 1.0 CA C:GLU62 4.5 25.5 1.0 CG C:GLU62 4.6 25.9 1.0 O C:HOH352 4.7 31.4 1.0 CB C:GLU27 4.8 20.0 1.0 CB C:GLU62 4.8 22.6 1.0 O C:HOH400 4.9 22.9 1.0 OE2 C:GLU107 4.9 21.6 1.0 CD C:GLN141 4.9 18.7 1.0

J.B.Bailey, L.Zhang, J.A.Chiong, S.Ahn, F.A.Tezcan. Synthetic Modularity of Protein-Metal-Organic Frameworks. J. Am. Chem. Soc. V. 139 8160 2017.
ISSN: ESSN 1520-5126
PubMed: 28590729
DOI: 10.1021/JACS.7B01202