Zinc in PDB 5up8: Crystal Structure of the Zn-Bound Human Heavy-Chain Variant 122H-Delta C-Star with Para-Benzenedihydroxamate

Enzymatic activity of Crystal Structure of the Zn-Bound Human Heavy-Chain Variant 122H-Delta C-Star with Para-Benzenedihydroxamate

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

Protein crystallography data

The structure of Crystal Structure of the Zn-Bound Human Heavy-Chain Variant 122H-Delta C-Star with Para-Benzenedihydroxamate, PDB code: 5up8 was solved by J.B.Bailey, L.Zhang, J.C.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) 49.27 / 2.63
Space group I 4 3 2
Cell size a, b, c (Å), α, β, γ (°) 155.810, 155.810, 155.810, 90.00, 90.00, 90.00
R / Rfree (%) 20.9 / 26.2

Other elements in 5up8:

The structure of Crystal Structure of the Zn-Bound Human Heavy-Chain Variant 122H-Delta C-Star with Para-Benzenedihydroxamate also contains other interesting chemical elements:

Sodium (Na) 1 atom

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of the Zn-Bound Human Heavy-Chain Variant 122H-Delta C-Star with Para-Benzenedihydroxamate (pdb code 5up8). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the Crystal Structure of the Zn-Bound Human Heavy-Chain Variant 122H-Delta C-Star with Para-Benzenedihydroxamate, PDB code: 5up8:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in 5up8

Go back to Zinc Binding Sites List in 5up8
Zinc binding site 1 out of 3 in the Crystal Structure of the Zn-Bound Human Heavy-Chain Variant 122H-Delta C-Star with Para-Benzenedihydroxamate


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 Zn-Bound Human Heavy-Chain Variant 122H-Delta C-Star with Para-Benzenedihydroxamate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn201

b:71.3
occ:1.00
 O A:HOH302 2.1 75.8 1.0
OE2 A:GLU62 2.1 66.0 1.0
OE2 A:GLU27 2.1 69.8 1.0
ND1 A:HIS65 2.4 93.1 1.0
CD A:GLU62 2.9 85.6 1.0
CD A:GLU27 2.9 80.7 1.0
OE1 A:GLU62 3.0 0.8 1.0
OE1 A:GLU27 3.1 71.8 1.0
ZN A:ZN202 3.2 0.6 1.0
CE1 A:HIS65 3.3 64.1 1.0
CG A:HIS65 3.4 84.4 1.0
OE1 A:GLN141 3.5 95.1 1.0
CB A:HIS65 3.7 74.8 1.0
CG1 A:VAL110 4.1 90.0 1.0
CG A:GLU62 4.3 63.4 1.0
CG A:GLU27 4.4 71.4 1.0
NE2 A:HIS65 4.4 1.0 1.0
CA A:GLU62 4.5 80.0 1.0
CD2 A:HIS65 4.5 87.7 1.0
CD A:GLN141 4.7 73.9 1.0
CB A:GLU62 4.7 63.1 1.0
CB A:GLU27 4.8 70.7 1.0

Zinc binding site 2 out of 3 in 5up8

Go back to Zinc Binding Sites List in 5up8
Zinc binding site 2 out of 3 in the Crystal Structure of the Zn-Bound Human Heavy-Chain Variant 122H-Delta C-Star with Para-Benzenedihydroxamate


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 Zn-Bound Human Heavy-Chain Variant 122H-Delta C-Star with Para-Benzenedihydroxamate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn202

b:0.6
occ:1.00
 OE1 A:GLU62 1.8 0.8 1.0
OE1 A:GLU107 2.5 80.8 1.0
OE2 A:GLU107 2.7 81.3 1.0
CD A:GLU107 2.9 86.8 1.0
CD A:GLU62 2.9 85.6 1.0
ZN A:ZN201 3.2 71.3 1.0
OE1 A:GLN141 3.4 95.1 1.0
OE2 A:GLU62 3.5 66.0 1.0
CE1 A:HIS65 4.1 64.1 1.0
CG A:GLU62 4.2 63.4 1.0
ND1 A:HIS65 4.2 93.1 1.0
CD A:GLN141 4.2 73.9 1.0
NE2 A:GLN141 4.3 65.9 1.0
O A:HOH302 4.3 75.8 1.0
CG A:GLU107 4.4 91.7 1.0
CE2 A:TYR34 4.6 77.5 1.0
OH A:TYR34 4.8 93.3 1.0
CB A:ALA144 4.9 60.8 1.0

Zinc binding site 3 out of 3 in 5up8

Go back to Zinc Binding Sites List in 5up8
Zinc binding site 3 out of 3 in the Crystal Structure of the Zn-Bound Human Heavy-Chain Variant 122H-Delta C-Star with Para-Benzenedihydroxamate


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 Zn-Bound Human Heavy-Chain Variant 122H-Delta C-Star with Para-Benzenedihydroxamate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn203

b:0.2
occ:0.33
 OAJ A:BYD205 2.1 82.3 0.2
NE2 A:HIS122 2.2 89.7 1.0
OAH A:BYD205 2.3 87.9 0.2
NAI A:BYD205 2.8 82.8 0.2
CAG A:BYD205 2.9 84.7 0.2
CE1 A:HIS122 3.1 0.4 1.0
CD2 A:HIS122 3.2 88.1 1.0
HAI A:BYD205 3.7 99.4 0.2
ND1 A:HIS122 4.2 0.3 1.0
CG A:HIS122 4.3 96.6 1.0
CAF A:BYD205 4.4 82.6 0.2
HAA A:BYD205 4.9 94.0 0.2

Reference:

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
Page generated: Wed Dec 16 11:06:09 2020

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