Cobalt in PDB 5vtd: Crystal Structure of the Co-Bound Human Heavy-Chain Ferritin Variant 122H-Delta C-Star

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

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

Protein crystallography data

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

Resolution Low / High (Å) 63.72 / 1.95
Space group F 4 3 2
Cell size a, b, c (Å), α, β, γ (°) 180.244, 180.244, 180.244, 90.00, 90.00, 90.00
R / Rfree (%) 17.4 / 21.7

Other elements in 5vtd:

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

Chlorine (Cl) 1 atom
Calcium (Ca) 3 atoms

Cobalt Binding Sites:

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

Cobalt binding site 1 out of 5 in 5vtd

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


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 1 of Crystal Structure of the Co-Bound Human Heavy-Chain Ferritin Variant 122H-Delta C-Star within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Co201

b:22.0
occ:0.33
 NE2 A:HIS122 2.1 19.7 1.0
O A:HOH440 2.2 29.4 1.0
CE1 A:HIS122 2.9 22.9 1.0
O A:HOH554 3.0 32.7 0.3
CD2 A:HIS122 3.2 20.9 1.0
ND1 A:HIS122 4.1 27.6 1.0
CG A:HIS122 4.3 23.4 1.0

Cobalt binding site 2 out of 5 in 5vtd

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


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 2 of Crystal Structure of the Co-Bound Human Heavy-Chain Ferritin Variant 122H-Delta C-Star within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Co202

b:22.1
occ:1.00
 OE2 A:GLU62 2.0 19.9 1.0
ND1 A:HIS65 2.1 14.1 1.0
OE1 A:GLU27 2.1 19.3 1.0
O A:HOH334 2.2 15.0 1.0
O A:HOH311 2.3 20.7 1.0
CD A:GLU62 2.9 18.7 1.0
CE1 A:HIS65 3.0 23.3 1.0
OE1 A:GLU62 3.0 23.2 1.0
CD A:GLU27 3.1 15.6 1.0
CG A:HIS65 3.2 17.2 1.0
OE2 A:GLU27 3.5 16.4 1.0
CB A:HIS65 3.6 11.9 1.0
OE1 A:GLN141 3.9 23.1 1.0
NE2 A:HIS65 4.2 20.2 1.0
O A:HOH406 4.2 20.4 1.0
O A:HOH438 4.2 29.3 1.0
CD2 A:HIS65 4.3 18.6 1.0
CG A:GLU62 4.3 12.9 1.0
CG1 A:VAL110 4.4 16.1 1.0
CG A:GLU27 4.4 11.5 1.0
CA A:GLU62 4.5 11.8 1.0
CB A:GLU62 4.6 14.1 1.0
CB A:GLU27 4.8 9.5 1.0
CD A:GLN141 4.8 20.8 1.0
OE2 A:GLU107 5.0 24.9 1.0

Cobalt binding site 3 out of 5 in 5vtd

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


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 3 of Crystal Structure of the Co-Bound Human Heavy-Chain Ferritin Variant 122H-Delta C-Star within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Co203

b:31.8
occ:0.50
 O A:HOH305 2.1 37.2 1.0
O A:HOH438 2.2 29.3 1.0
OE1 A:GLU107 2.4 24.4 1.0
OE1 A:GLU62 2.5 23.2 1.0
OE1 A:GLN58 3.1 37.5 1.0
O A:HOH374 3.3 36.1 1.0
CD A:GLU107 3.4 23.2 1.0
O A:HOH311 3.6 20.7 1.0
OE2 A:GLU107 3.7 24.9 1.0
CD A:GLU62 3.7 18.7 1.0
OH A:TYR34 4.1 20.4 1.0
CE2 A:TYR34 4.2 12.0 1.0
O A:HOH494 4.2 42.7 1.0
CD A:GLN58 4.3 27.2 1.0
O A:HOH470 4.3 41.0 1.0
CG A:GLU62 4.3 12.9 1.0
CB A:ALA144 4.4 12.6 1.0
CZ A:TYR34 4.5 20.2 1.0
CE1 A:HIS65 4.6 23.3 1.0
CG A:GLU107 4.6 16.3 1.0
OE2 A:GLU62 4.7 19.9 1.0
O A:HOH461 4.8 27.2 1.0
CB A:GLN58 4.8 12.2 1.0
OE1 A:GLN141 5.0 23.1 1.0

Cobalt binding site 4 out of 5 in 5vtd

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


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 4 of Crystal Structure of the Co-Bound Human Heavy-Chain Ferritin Variant 122H-Delta C-Star within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Co204

b:17.9
occ:0.25
 O A:HOH448 2.0 19.1 0.2
NE2 A:HIS173 2.3 11.2 1.0
CL A:CL206 2.5 13.2 0.2
CE1 A:HIS173 3.1 13.2 1.0
CD2 A:HIS173 3.3 14.1 1.0
ND1 A:HIS173 4.3 11.4 1.0
CG A:HIS173 4.4 12.2 1.0

Cobalt binding site 5 out of 5 in 5vtd

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


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 5 of Crystal Structure of the Co-Bound Human Heavy-Chain Ferritin Variant 122H-Delta C-Star within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Co205

b:20.5
occ:0.50
 O A:HOH516 2.7 27.2 1.0
N A:TYR12 3.3 10.2 1.0
N A:ASN11 3.4 11.6 1.0
O A:TYR12 3.6 14.7 1.0
CG A:ARG9 3.7 14.4 1.0
NE A:ARG9 3.7 16.6 1.0
O A:HOH412 3.7 18.9 1.0
CD A:ARG9 3.7 19.9 1.0
C A:GLN10 4.0 13.8 1.0
C A:TYR12 4.1 11.8 1.0
CA A:GLN10 4.1 11.7 1.0
CA A:TYR12 4.1 10.6 1.0
CA A:ASN11 4.1 12.9 1.0
N A:GLN10 4.2 13.7 1.0
C A:ASN11 4.2 9.7 1.0
C A:ARG9 4.3 15.5 1.0
CB A:TYR12 4.4 9.3 1.0
O A:ARG9 4.5 13.9 1.0
CB A:ARG9 4.6 13.2 1.0
O A:GLN10 4.9 11.4 1.0
O A:HOH495 4.9 29.6 1.0
CZ A:ARG9 4.9 17.3 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: Sun Dec 13 10:48:51 2020

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