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Calcium in PDB 6b8f: Contracted Human Heavy-Chain Ferritin Crystal-Hydrogel Hybrid

Enzymatic activity of Contracted Human Heavy-Chain Ferritin Crystal-Hydrogel Hybrid

All present enzymatic activity of Contracted Human Heavy-Chain Ferritin Crystal-Hydrogel Hybrid:
1.16.3.1;

Protein crystallography data

The structure of Contracted Human Heavy-Chain Ferritin Crystal-Hydrogel Hybrid, PDB code: 6b8f was solved by L.Zhang, J.B.Bailey, R.Subramanian, F.A.Tezcan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 45.01 / 1.06
Space group F 4 3 2
Cell size a, b, c (Å), α, β, γ (°) 180.040, 180.040, 180.040, 90.00, 90.00, 90.00
R / Rfree (%) 9.1 / 10.3

Other elements in 6b8f:

The structure of Contracted Human Heavy-Chain Ferritin Crystal-Hydrogel Hybrid also contains other interesting chemical elements:

Iron (Fe) 2 atoms

Calcium Binding Sites:

Pages:

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

Binding sites:

The binding sites of Calcium atom in the Contracted Human Heavy-Chain Ferritin Crystal-Hydrogel Hybrid (pdb code 6b8f). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 11 binding sites of Calcium where determined in the Contracted Human Heavy-Chain Ferritin Crystal-Hydrogel Hybrid, PDB code: 6b8f:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Calcium binding site 1 out of 11 in 6b8f

Go back to Calcium Binding Sites List in 6b8f
Calcium binding site 1 out of 11 in the Contracted Human Heavy-Chain Ferritin Crystal-Hydrogel Hybrid


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Contracted Human Heavy-Chain Ferritin Crystal-Hydrogel Hybrid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca203

b:6.8
occ:0.28
 O A:HOH325 1.8 25.6 0.3
OE2 A:GLU134 2.1 7.8 0.3
OD1 A:ASP131 2.3 14.6 0.7
OE2 A:GLU134 2.4 17.7 0.7
CD A:GLU134 3.2 8.0 0.3
CG A:ASP131 3.3 11.6 0.7
HB2 A:ASP131 3.4 11.7 0.7
O A:HOH328 3.5 6.7 0.9
CD A:GLU134 3.6 15.2 0.7
HA A:ASP131 3.6 11.3 0.3
HG3 A:GLU134 3.7 9.4 0.3
OD1 A:ASP131 3.7 7.9 0.3
CB A:ASP131 3.9 9.8 0.7
HA A:ASP131 3.9 12.9 0.7
CG A:GLU134 4.0 7.8 0.3
OE1 A:GLU134 4.0 18.2 0.7
HG2 A:GLU134 4.1 9.4 0.3
OE1 A:GLU134 4.2 11.1 0.3
HB2 A:ASP131 4.2 9.1 0.3
OD2 A:ASP131 4.2 13.2 0.7
HB2 A:GLU134 4.3 17.8 0.7
CA A:ASP131 4.5 9.4 0.3
CA A:ASP131 4.5 10.8 0.7
HB3 A:GLU134 4.5 17.8 0.7
HG1 A:THR135 4.6 24.4 1.0
O A:HOH310 4.6 29.0 1.0
CB A:ASP131 4.6 7.6 0.3
CG A:ASP131 4.6 6.9 0.3
HB3 A:ASP131 4.7 11.7 0.7
CG A:GLU134 4.7 15.1 0.7
CB A:GLU134 4.7 14.8 0.7
OG1 A:THR135 5.0 20.3 1.0

Calcium binding site 2 out of 11 in 6b8f

Go back to Calcium Binding Sites List in 6b8f
Calcium binding site 2 out of 11 in the Contracted Human Heavy-Chain Ferritin Crystal-Hydrogel Hybrid


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Contracted Human Heavy-Chain Ferritin Crystal-Hydrogel Hybrid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca204

b:12.7
occ:0.68
 H A:TYR12 2.4 7.5 1.0
O A:HOH523 2.7 40.2 1.0
HG2 A:ARG9 2.9 9.0 1.0
H A:ASN11 3.1 7.7 1.0
O A:HOH560 3.1 31.5 0.9
HE A:ARG9 3.1 13.9 1.0
O A:HOH518 3.2 42.7 1.0
HD3 A:ARG9 3.2 15.6 1.0
N A:TYR12 3.3 6.2 1.0
N A:ASN11 3.4 6.4 1.0
O A:TYR12 3.5 8.1 1.0
HA A:GLN10 3.6 7.6 1.0
CG A:ARG9 3.7 7.5 1.0
CD A:ARG9 3.7 13.0 1.0
NE A:ARG9 3.7 11.6 1.0
O A:HOH500 3.9 20.8 1.0
HB3 A:TYR12 3.9 7.6 1.0
C A:GLN10 3.9 6.0 1.0
CA A:GLN10 4.0 6.4 1.0
N A:GLN10 4.0 5.9 1.0
HA A:ASN11 4.1 7.9 1.0
C A:TYR12 4.1 6.0 1.0
CA A:TYR12 4.1 6.1 1.0
CA A:ASN11 4.1 6.6 1.0
C A:ASN11 4.2 6.3 1.0
H A:GLN10 4.2 7.1 1.0
C A:ARG9 4.3 6.6 1.0
HG3 A:ARG9 4.3 9.0 1.0
HB3 A:ARG9 4.3 9.4 1.0
CB A:TYR12 4.4 6.3 1.0
O A:ARG9 4.4 8.7 1.0
CB A:ARG9 4.5 7.9 1.0
O A:HOH604 4.6 32.1 0.9
O A:HOH610 4.6 36.2 0.9
HD2 A:ARG9 4.6 15.6 1.0
HB2 A:TYR12 4.6 7.6 1.0
O A:GLN10 4.8 6.2 1.0
CZ A:ARG9 4.9 8.9 1.0
HH21 A:ARG9 4.9 11.1 1.0

Calcium binding site 3 out of 11 in 6b8f

Go back to Calcium Binding Sites List in 6b8f
Calcium binding site 3 out of 11 in the Contracted Human Heavy-Chain Ferritin Crystal-Hydrogel Hybrid


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Contracted Human Heavy-Chain Ferritin Crystal-Hydrogel Hybrid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca205

b:17.9
occ:0.65
 H A:GLN14 2.3 7.8 1.0
HG2 A:GLN14 2.7 11.5 0.4
O A:HOH610 2.9 36.2 0.9
HA A:HIS13 2.9 7.7 1.0
HG3 A:GLN14 3.0 19.6 0.3
HG2 A:GLN14 3.0 12.0 0.3
O A:HOH392 3.1 40.3 1.0
O A:HOH518 3.1 42.7 1.0
N A:GLN14 3.2 6.5 1.0
CG A:GLN14 3.4 9.6 0.4
HB2 A:GLN14 3.4 14.8 0.3
HB2 A:GLN14 3.5 8.8 0.4
HB3 A:GLN14 3.5 9.7 0.3
HG3 A:GLN14 3.5 11.5 0.4
CG A:GLN14 3.7 16.3 0.3
CD2 A:HIS13 3.7 9.3 1.0
CG A:HIS13 3.7 7.0 1.0
CA A:HIS13 3.8 6.4 1.0
CG A:GLN14 3.8 10.0 0.3
CB A:GLN14 3.8 7.3 0.4
NE2 A:HIS13 3.8 10.5 1.0
CB A:GLN14 3.9 12.3 0.3
ND1 A:HIS13 3.9 7.7 1.0
CE1 A:HIS13 3.9 9.1 1.0
C A:HIS13 3.9 6.0 1.0
CB A:GLN14 3.9 8.1 0.3
HD2 A:HIS13 4.0 11.1 1.0
CA A:GLN14 4.1 5.9 0.4
CA A:GLN14 4.1 8.2 0.3
CA A:GLN14 4.1 7.0 0.3
CD A:GLN14 4.2 19.1 0.3
O A:HOH327 4.2 42.0 1.0
HE2 A:HIS13 4.2 12.6 1.0
CB A:HIS13 4.3 6.8 1.0
HE21 A:GLN14 4.4 14.7 0.4
HE1 A:HIS13 4.4 10.9 1.0
OE1 A:GLN14 4.4 20.9 0.3
HG3 A:GLN14 4.5 12.0 0.3
HG2 A:GLN14 4.5 19.6 0.3
CD A:GLN14 4.5 14.6 0.3
O A:TYR12 4.6 8.1 1.0
HA A:GLN14 4.6 7.1 0.4
HA A:GLN14 4.7 9.8 0.3
HA A:GLN14 4.7 8.4 0.3
CD A:GLN14 4.7 10.9 0.4
HB3 A:GLN14 4.7 8.8 0.4
H A:ASP15 4.8 7.6 1.0
HH21 A:ARG9 4.8 11.1 1.0
HB2 A:HIS13 4.8 8.2 1.0
HB3 A:GLN14 4.8 14.8 0.3
NE2 A:GLN14 4.8 20.3 0.3
HB2 A:GLN14 4.9 9.7 0.3
N A:HIS13 4.9 6.1 1.0
NE2 A:GLN14 4.9 12.2 0.4
O A:HOH573 5.0 21.5 1.0
HE21 A:GLN14 5.0 17.9 0.3
HE21 A:GLN14 5.0 24.4 0.3

Calcium binding site 4 out of 11 in 6b8f

Go back to Calcium Binding Sites List in 6b8f
Calcium binding site 4 out of 11 in the Contracted Human Heavy-Chain Ferritin Crystal-Hydrogel Hybrid


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Contracted Human Heavy-Chain Ferritin Crystal-Hydrogel Hybrid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca206

b:16.8
occ:0.54
 O A:HOH526 2.4 11.0 0.9
HD22 A:ASN21 2.5 7.3 1.0
HA A:ALA18 2.7 7.2 1.0
O A:HOH344 3.0 9.1 0.7
O A:HOH434 3.1 10.9 1.0
HB2 A:ALA18 3.3 8.3 1.0
ND2 A:ASN21 3.3 6.1 1.0
HG2 A:GLU17 3.3 7.5 1.0
HD21 A:ASN21 3.5 7.3 1.0
CA A:ALA18 3.5 6.0 1.0
CB A:ALA18 3.8 6.9 1.0
N A:ALA18 3.8 5.4 1.0
HD2 A:PHE81 3.9 11.1 1.0
O A:HOH587 4.0 29.3 0.9
HB1 A:ALA18 4.0 8.3 1.0
HB2 A:ASN21 4.0 6.2 1.0
H A:ALA18 4.2 6.5 1.0
C A:GLU17 4.2 5.3 1.0
CG A:GLU17 4.2 6.3 1.0
O A:GLU17 4.2 5.6 1.0
O A:HOH305 4.3 12.9 0.7
CG A:ASN21 4.4 5.3 1.0
O A:HOH430 4.5 18.9 0.9
HB2 A:PHE81 4.6 7.7 1.0
HB3 A:GLU17 4.6 7.1 1.0
CD A:GLU17 4.6 7.2 1.0
CD2 A:PHE81 4.6 9.2 1.0
HB3 A:ALA18 4.7 8.3 1.0
CB A:ASN21 4.7 5.1 1.0
OE2 A:GLU17 4.7 7.4 1.0
C A:ALA18 4.7 5.7 1.0
O A:HOH579 4.8 22.0 1.0
HG3 A:GLU17 4.8 7.5 1.0
O A:ARG79 4.8 6.5 1.0
CB A:GLU17 4.9 5.9 1.0
O A:ALA18 5.0 6.0 1.0

Calcium binding site 5 out of 11 in 6b8f

Go back to Calcium Binding Sites List in 6b8f
Calcium binding site 5 out of 11 in the Contracted Human Heavy-Chain Ferritin Crystal-Hydrogel Hybrid


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Contracted Human Heavy-Chain Ferritin Crystal-Hydrogel Hybrid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca207

b:5.0
occ:0.22
 CA A:CA211 1.2 6.0 0.3
OD1 A:ASP84 2.3 8.5 1.0
OD2 A:ASP84 2.6 14.8 1.0
CG A:ASP84 2.8 7.2 1.0
CB A:ASP84 4.3 5.8 1.0
HB3 A:ASP84 4.6 6.9 1.0
HB2 A:ASP84 4.7 6.9 1.0
O A:HOH364 4.8 10.8 1.0
H A:ASP84 4.8 5.5 1.0
HA A:ASP84 4.9 5.6 1.0
O A:HOH332 5.0 31.6 0.5

Calcium binding site 6 out of 11 in 6b8f

Go back to Calcium Binding Sites List in 6b8f
Calcium binding site 6 out of 11 in the Contracted Human Heavy-Chain Ferritin Crystal-Hydrogel Hybrid


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Contracted Human Heavy-Chain Ferritin Crystal-Hydrogel Hybrid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca208

b:7.5
occ:0.20
 HD22 A:LEU169 3.1 9.2 1.0
NE2 A:HIS173 3.1 9.0 0.7
NE2 A:HIS173 3.3 8.7 0.3
HD21 A:LEU169 3.9 9.2 1.0
CD2 A:LEU169 3.9 7.7 1.0
CE1 A:HIS173 4.0 9.3 0.7
CD2 A:HIS173 4.0 8.2 0.7
HE1 A:HIS173 4.1 11.2 0.7
CE1 A:HIS173 4.1 10.5 0.3
HD2 A:HIS173 4.1 9.9 0.7
HE1 A:HIS173 4.1 12.6 0.3
HD13 A:LEU169 4.2 9.8 1.0
CD2 A:HIS173 4.2 8.8 0.3
HD2 A:HIS173 4.3 10.6 0.3
HD23 A:LEU169 4.5 9.2 1.0
HD11 A:LEU169 4.7 9.8 1.0
CD1 A:LEU169 4.8 8.2 1.0
CG A:LEU169 4.9 6.5 1.0
HB3 A:LEU169 5.0 7.0 1.0

Calcium binding site 7 out of 11 in 6b8f

Go back to Calcium Binding Sites List in 6b8f
Calcium binding site 7 out of 11 in the Contracted Human Heavy-Chain Ferritin Crystal-Hydrogel Hybrid


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Contracted Human Heavy-Chain Ferritin Crystal-Hydrogel Hybrid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca209

b:16.8
occ:0.61
 HE22 A:GLN75 2.4 10.8 1.0
O A:HOH530 2.8 34.0 0.9
O A:HOH338 3.1 19.5 0.9
NE2 A:GLN75 3.3 9.0 1.0
HE2 A:LYS71 3.4 17.7 0.6
HE3 A:LYS71 3.6 10.2 0.4
HE21 A:GLN75 3.7 10.8 1.0
HE2 A:PHE132 3.7 14.4 0.3
HE2 A:LYS71 3.8 10.2 0.4
HZ2 A:LYS71 3.8 20.4 0.6
HZ1 A:LYS71 4.0 20.4 0.6
CE A:LYS71 4.1 8.5 0.4
NZ A:LYS71 4.2 17.0 0.6
O A:HOH507 4.2 26.8 1.0
CD A:GLN75 4.2 7.0 1.0
CE A:LYS71 4.2 14.8 0.6
OE1 A:GLN75 4.3 8.0 1.0
HZ3 A:LYS68 4.5 21.0 0.5
O A:HOH481 4.5 8.4 0.8
HZ1 A:LYS68 4.6 21.0 0.5
CE2 A:PHE132 4.6 12.0 0.3
HE3 A:LYS71 4.7 17.7 0.6
HD3 A:LYS71 4.8 7.0 0.4
HZ A:PHE132 4.9 14.8 0.3
HZ3 A:LYS71 5.0 12.1 0.4
NZ A:LYS68 5.0 17.5 0.5

Calcium binding site 8 out of 11 in 6b8f

Go back to Calcium Binding Sites List in 6b8f
Calcium binding site 8 out of 11 in the Contracted Human Heavy-Chain Ferritin Crystal-Hydrogel Hybrid


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Contracted Human Heavy-Chain Ferritin Crystal-Hydrogel Hybrid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca210

b:6.9
occ:0.39
 O A:HOH487 2.4 8.8 0.8
O A:HOH512 2.5 8.7 0.8
O A:HOH448 2.5 7.3 0.7
O A:HOH358 2.5 7.7 0.9
HA A:ASP89 3.8 6.8 1.0
CA A:CA212 3.8 7.4 0.2
HZ1 A:LYS87 3.9 14.5 0.4
HZ3 A:LYS87 4.1 14.5 0.4
O A:ASP89 4.4 7.6 1.0
NZ A:LYS87 4.4 12.1 0.4
HE3 A:LYS87 4.5 11.5 0.6
O A:HOH467 4.5 7.9 0.9
HE2 A:LYS87 4.6 11.5 0.6
HE3 A:LYS87 4.7 13.2 0.4
CA A:ASP89 4.7 5.7 1.0
O A:HOH427 4.7 8.9 0.9
O A:HOH589 4.7 12.3 0.9
OD1 A:ASP89 4.7 8.5 1.0
C A:ASP89 4.8 5.8 1.0
O A:HOH440 4.9 10.1 0.8
O A:HOH472 4.9 7.6 0.7
O A:PRO88 4.9 6.0 1.0
CE A:LYS87 5.0 9.6 0.6

Calcium binding site 9 out of 11 in 6b8f

Go back to Calcium Binding Sites List in 6b8f
Calcium binding site 9 out of 11 in the Contracted Human Heavy-Chain Ferritin Crystal-Hydrogel Hybrid


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 9 of Contracted Human Heavy-Chain Ferritin Crystal-Hydrogel Hybrid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca211

b:6.0
occ:0.28
 CA A:CA207 1.2 5.0 0.2
OD2 A:ASP84 2.1 14.8 1.0
OD1 A:ASP84 2.7 8.5 1.0
CG A:ASP84 2.8 7.2 1.0
O A:HOH332 4.1 31.6 0.5
CB A:ASP84 4.2 5.8 1.0
HB2 A:ASP84 4.4 6.9 1.0
O A:HOH364 4.5 10.8 1.0
HB3 A:ASP84 4.6 6.9 1.0
H A:ASP84 4.9 5.5 1.0

Calcium binding site 10 out of 11 in 6b8f

Go back to Calcium Binding Sites List in 6b8f
Calcium binding site 10 out of 11 in the Contracted Human Heavy-Chain Ferritin Crystal-Hydrogel Hybrid


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 10 of Contracted Human Heavy-Chain Ferritin Crystal-Hydrogel Hybrid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca212

b:7.4
occ:0.25
 O A:HOH432 2.4 8.9 0.8
O A:HOH467 2.4 7.9 0.9
O A:HOH358 2.4 7.7 0.9
CA A:CA213 3.5 9.6 0.2
O A:HOH512 3.7 8.7 0.8
CA A:CA210 3.8 6.9 0.4
O A:ASP89 3.9 7.6 1.0
O A:HOH624 4.3 14.0 0.9
O A:HOH437 4.3 13.2 0.8
O A:HOH589 4.4 12.3 0.9
OE1 A:GLU90 4.4 7.7 1.0
OE2 A:GLU90 4.5 8.8 1.0
CD A:GLU90 4.7 7.2 1.0
HA A:GLU90 5.0 6.3 1.0

Reference:

L.Zhang, J.B.Bailey, R.H.Subramanian, F.A.Tezcan. Hyperexpandable, Self-Healing Macromolecular Crystals with Integrated Polymer Networks. Nature V. 557 86 2018.
ISSN: ESSN 1476-4687
PubMed: 29720635
DOI: 10.1038/S41586-018-0057-7
Page generated: Mon Jul 15 16:43:20 2024

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