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Nickel in PDB 5up7: Crystal Structure of the Ni-Bound Human Heavy-Chain Ferritin 122H- Delta C-Star Variant

Enzymatic activity of Crystal Structure of the Ni-Bound Human Heavy-Chain Ferritin 122H- Delta C-Star Variant

All present enzymatic activity of Crystal Structure of the Ni-Bound Human Heavy-Chain Ferritin 122H- Delta C-Star Variant:
1.16.3.1;

Protein crystallography data

The structure of Crystal Structure of the Ni-Bound Human Heavy-Chain Ferritin 122H- Delta C-Star Variant, PDB code: 5up7 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) 52.01 / 1.79
Space group F 4 3 2
Cell size a, b, c (Å), α, β, γ (°) 180.150, 180.150, 180.150, 90.00, 90.00, 90.00
R / Rfree (%) 15.9 / n/a

Other elements in 5up7:

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

Calcium (Ca) 2 atoms
Chlorine (Cl) 1 atom

Nickel Binding Sites:

The binding sites of Nickel atom in the Crystal Structure of the Ni-Bound Human Heavy-Chain Ferritin 122H- Delta C-Star Variant (pdb code 5up7). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 5 binding sites of Nickel where determined in the Crystal Structure of the Ni-Bound Human Heavy-Chain Ferritin 122H- Delta C-Star Variant, PDB code: 5up7:
Jump to Nickel binding site number: 1; 2; 3; 4; 5;

Nickel binding site 1 out of 5 in 5up7

Go back to Nickel Binding Sites List in 5up7
Nickel binding site 1 out of 5 in the Crystal Structure of the Ni-Bound Human Heavy-Chain Ferritin 122H- Delta C-Star Variant


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of Crystal Structure of the Ni-Bound Human Heavy-Chain Ferritin 122H- Delta C-Star Variant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni201

b:13.1
occ:1.00
 OE2 A:GLU62 2.0 15.0 1.0
OE1 A:GLU27 2.1 10.8 1.0
ND1 A:HIS65 2.1 14.9 1.0
O A:HOH312 2.1 22.2 1.0
O A:HOH348 2.2 11.1 1.0
CD A:GLU62 2.9 10.6 1.0
CE1 A:HIS65 3.0 13.4 1.0
CD A:GLU27 3.1 9.0 1.0
OE1 A:GLU62 3.1 18.0 1.0
CG A:HIS65 3.2 8.5 1.0
OE2 A:GLU27 3.4 10.9 1.0
CB A:HIS65 3.5 7.2 1.0
O A:HOH384 4.0 18.2 1.0
OE1 A:GLN141 4.1 21.8 1.0
NE2 A:HIS65 4.1 16.9 1.0
CD2 A:HIS65 4.2 15.2 1.0
CG A:GLU62 4.3 9.0 1.0
CG1 A:VAL110 4.4 13.2 1.0
CG A:GLU27 4.4 8.5 1.0
O A:HOH425 4.5 22.7 1.0
CA A:GLU62 4.5 10.2 1.0
CB A:GLU62 4.6 7.6 1.0
CB A:GLU27 4.7 7.2 1.0
CD A:GLN141 4.9 14.6 1.0

Nickel binding site 2 out of 5 in 5up7

Go back to Nickel Binding Sites List in 5up7
Nickel binding site 2 out of 5 in the Crystal Structure of the Ni-Bound Human Heavy-Chain Ferritin 122H- Delta C-Star Variant


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of Crystal Structure of the Ni-Bound Human Heavy-Chain Ferritin 122H- Delta C-Star Variant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni202

b:31.2
occ:0.50
 O A:HOH443 1.8 33.4 1.0
O A:HOH310 2.0 27.9 1.0
O A:HOH425 2.2 22.7 1.0
OE1 A:GLU107 2.5 18.4 1.0
OE1 A:GLU62 2.6 18.0 1.0
O A:HOH467 2.7 28.4 1.0
CD A:GLU107 3.4 17.5 1.0
O A:HOH312 3.6 22.2 1.0
OE2 A:GLU107 3.6 21.3 1.0
CD A:GLN58 3.8 25.2 1.0
CD A:GLU62 3.8 10.6 1.0
O A:HOH525 3.9 31.5 1.0
OE2 A:GLU140 4.2 18.4 0.5
OH A:TYR34 4.2 13.3 1.0
OE1 A:GLU61 4.2 27.2 0.5
NE2 A:GLN58 4.2 20.0 1.0
CE2 A:TYR34 4.3 9.6 1.0
CB A:ALA144 4.3 11.5 1.0
CG A:GLU62 4.5 9.0 1.0
CE1 A:HIS65 4.5 13.4 1.0
CZ A:TYR34 4.6 13.2 1.0
CG A:GLU107 4.7 8.0 1.0
OE2 A:GLU62 4.7 15.0 1.0
O A:HOH497 4.9 18.6 1.0
CG A:GLN58 4.9 13.0 1.0
CB A:GLN58 5.0 10.7 1.0

Nickel binding site 3 out of 5 in 5up7

Go back to Nickel Binding Sites List in 5up7
Nickel binding site 3 out of 5 in the Crystal Structure of the Ni-Bound Human Heavy-Chain Ferritin 122H- Delta C-Star Variant


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 3 of Crystal Structure of the Ni-Bound Human Heavy-Chain Ferritin 122H- Delta C-Star Variant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni203

b:12.0
occ:0.33
 NE2 A:HIS122 2.1 12.3 1.0
O A:HOH481 2.1 19.5 1.0
CE1 A:HIS122 2.9 14.1 1.0
CD2 A:HIS122 3.2 11.9 1.0
O A:HOH615 3.2 29.1 0.3
ND1 A:HIS122 4.1 13.9 1.0
CG A:HIS122 4.2 12.1 1.0
O A:HOH487 4.3 22.7 1.0
O A:HOH326 4.9 27.4 1.0

Nickel binding site 4 out of 5 in 5up7

Go back to Nickel Binding Sites List in 5up7
Nickel binding site 4 out of 5 in the Crystal Structure of the Ni-Bound Human Heavy-Chain Ferritin 122H- Delta C-Star Variant


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 4 of Crystal Structure of the Ni-Bound Human Heavy-Chain Ferritin 122H- Delta C-Star Variant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni204

b:9.9
occ:0.25
 O A:HOH484 2.1 10.4 0.2
NE2 A:HIS173 2.2 8.4 1.0
CL A:CL208 2.4 9.6 0.2
CE1 A:HIS173 3.1 8.6 1.0
CD2 A:HIS173 3.2 10.6 1.0
ND1 A:HIS173 4.2 10.8 1.0
CG A:HIS173 4.3 8.3 1.0
O A:HOH575 4.5 30.6 1.0

Nickel binding site 5 out of 5 in 5up7

Go back to Nickel Binding Sites List in 5up7
Nickel binding site 5 out of 5 in the Crystal Structure of the Ni-Bound Human Heavy-Chain Ferritin 122H- Delta C-Star Variant


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 5 of Crystal Structure of the Ni-Bound Human Heavy-Chain Ferritin 122H- Delta C-Star Variant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni205

b:42.4
occ:0.50
 NE2 A:HIS105 2.4 24.5 1.0
CD2 A:HIS105 3.1 17.7 1.0
O A:HOH489 3.2 40.5 1.0
CE1 A:HIS105 3.5 25.1 1.0
O A:HOH562 4.2 37.7 1.0
CG A:HIS105 4.3 17.8 1.0
O A:HOH625 4.4 41.4 1.0
ND1 A:HIS105 4.5 25.5 1.0
O A:HOH420 4.7 20.6 1.0
O A:HOH600 4.8 25.7 1.0

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: Thu Oct 10 08:06:27 2024

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