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Calcium in PDB 6wyf: Crystal Structure of Human H-Chain Ferritin Variant 157C Delta C-Star Modified with A Raft Agent Soaked in An Acrylate Solution

Enzymatic activity of Crystal Structure of Human H-Chain Ferritin Variant 157C Delta C-Star Modified with A Raft Agent Soaked in An Acrylate Solution

All present enzymatic activity of Crystal Structure of Human H-Chain Ferritin Variant 157C Delta C-Star Modified with A Raft Agent Soaked in An Acrylate Solution:
1.16.3.1;

Protein crystallography data

The structure of Crystal Structure of Human H-Chain Ferritin Variant 157C Delta C-Star Modified with A Raft Agent Soaked in An Acrylate Solution, PDB code: 6wyf was solved by J.B.Bailey, L.Zhang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 36.73 / 1.25
Space group F 4 3 2
Cell size a, b, c (Å), α, β, γ (°) 179.940, 179.940, 179.940, 90.00, 90.00, 90.00
R / Rfree (%) 11.3 / 13.1

Other elements in 6wyf:

The structure of Crystal Structure of Human H-Chain Ferritin Variant 157C Delta C-Star Modified with A Raft Agent Soaked in An Acrylate Solution also contains other interesting chemical elements:

Iron (Fe) 2 atoms
Sodium (Na) 1 atom

Calcium Binding Sites:

Pages:

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

Binding sites:

The binding sites of Calcium atom in the Crystal Structure of Human H-Chain Ferritin Variant 157C Delta C-Star Modified with A Raft Agent Soaked in An Acrylate Solution (pdb code 6wyf). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 11 binding sites of Calcium where determined in the Crystal Structure of Human H-Chain Ferritin Variant 157C Delta C-Star Modified with A Raft Agent Soaked in An Acrylate Solution, PDB code: 6wyf:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Calcium binding site 1 out of 11 in 6wyf

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Calcium binding site 1 out of 11 in the Crystal Structure of Human H-Chain Ferritin Variant 157C Delta C-Star Modified with A Raft Agent Soaked in An Acrylate Solution


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Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of Human H-Chain Ferritin Variant 157C Delta C-Star Modified with A Raft Agent Soaked in An Acrylate Solution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca202

b:10.0
occ:0.30
 CA A:CA212 1.2 7.4 0.2
OD2 A:ASP84 2.1 17.1 1.0
O A:HOH532 2.4 17.9 0.5
OD1 A:ASP84 2.7 11.7 1.0
CG A:ASP84 2.8 11.5 1.0
O A:HOH327 4.1 30.0 0.5
CB A:ASP84 4.2 9.0 1.0
HB2 A:ASP84 4.5 10.8 1.0
O A:HOH333 4.5 13.9 1.0
HB3 A:ASP84 4.6 10.8 1.0
H A:ASP84 4.9 8.9 1.0

Calcium binding site 2 out of 11 in 6wyf

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Calcium binding site 2 out of 11 in the Crystal Structure of Human H-Chain Ferritin Variant 157C Delta C-Star Modified with A Raft Agent Soaked in An Acrylate Solution


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Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of Human H-Chain Ferritin Variant 157C Delta C-Star Modified with A Raft Agent Soaked in An Acrylate Solution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca203

b:12.2
occ:0.20
 HD22 A:LEU169 3.1 14.6 1.0
NE2 A:HIS173 3.1 14.0 0.5
NE2 A:HIS173 3.2 16.7 0.5
HD21 A:LEU169 3.9 14.6 1.0
CD2 A:LEU169 3.9 12.2 1.0
HD13 A:LEU169 4.0 15.4 1.0
CE1 A:HIS173 4.0 11.8 0.5
CD2 A:HIS173 4.1 12.2 0.5
CE1 A:HIS173 4.1 16.7 0.5
HE1 A:HIS173 4.1 14.2 0.5
HE1 A:HIS173 4.1 20.0 0.5
HD2 A:HIS173 4.2 14.6 0.5
CD2 A:HIS173 4.2 15.3 0.5
HD2 A:HIS173 4.3 18.3 0.5
HD23 A:LEU169 4.5 14.6 1.0
CD1 A:LEU169 4.7 12.8 1.0
HD11 A:LEU169 4.8 15.4 1.0
CG A:LEU169 4.9 10.9 1.0
HB3 A:LEU169 4.9 11.8 1.0

Calcium binding site 3 out of 11 in 6wyf

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Calcium binding site 3 out of 11 in the Crystal Structure of Human H-Chain Ferritin Variant 157C Delta C-Star Modified with A Raft Agent Soaked in An Acrylate Solution


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of Human H-Chain Ferritin Variant 157C Delta C-Star Modified with A Raft Agent Soaked in An Acrylate Solution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca204

b:22.6
occ:0.65
 H A:GLN14 2.3 11.9 1.0
HG2 A:GLN14 2.7 27.1 1.0
HA A:HIS13 2.9 11.1 1.0
O A:HOH505 3.0 46.2 1.0
O A:HOH558 3.0 41.2 1.0
O A:HOH553 3.0 42.4 1.0
N A:GLN14 3.2 9.9 1.0
CG A:GLN14 3.4 22.6 1.0
HG3 A:GLN14 3.5 27.1 1.0
HB2 A:GLN14 3.6 18.3 1.0
CD2 A:HIS13 3.7 14.1 1.0
CG A:HIS13 3.7 11.2 1.0
CA A:HIS13 3.8 9.3 1.0
NE2 A:HIS13 3.9 15.1 1.0
CB A:GLN14 3.9 15.3 1.0
ND1 A:HIS13 3.9 11.4 1.0
CE1 A:HIS13 4.0 13.6 1.0
C A:HIS13 4.0 9.4 1.0
HD2 A:HIS13 4.0 16.8 1.0
CA A:GLN14 4.1 11.0 1.0
O A:HOH310 4.2 43.3 1.0
HE2 A:HIS13 4.2 18.1 1.0
HE21 A:GLN14 4.3 36.4 1.0
CB A:HIS13 4.3 10.6 1.0
HE1 A:HIS13 4.4 16.3 1.0
O A:TYR12 4.6 11.7 1.0
HA A:GLN14 4.6 13.1 1.0
CD A:GLN14 4.7 26.4 1.0
H A:ASP15 4.8 11.8 1.0
HB2 A:HIS13 4.8 12.7 1.0
HB3 A:GLN14 4.8 18.3 1.0
HH21 A:ARG9 4.8 15.8 1.0
NE2 A:GLN14 4.8 30.4 1.0
N A:HIS13 4.9 9.7 1.0

Calcium binding site 4 out of 11 in 6wyf

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Calcium binding site 4 out of 11 in the Crystal Structure of Human H-Chain Ferritin Variant 157C Delta C-Star Modified with A Raft Agent Soaked in An Acrylate Solution


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystal Structure of Human H-Chain Ferritin Variant 157C Delta C-Star Modified with A Raft Agent Soaked in An Acrylate Solution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca205

b:13.0
occ:0.17
 O A:HOH414 2.4 15.1 1.0
O A:HOH420 2.4 23.0 1.0
O A:HOH602 2.4 27.5 1.0
CA A:CA206 3.5 9.6 0.2
O A:HOH443 4.3 12.2 1.0
O A:HOH389 4.4 27.2 1.0
OE2 A:GLU90 4.4 13.4 1.0
OE1 A:GLU90 4.5 12.2 1.0
O A:HOH608 4.6 19.2 1.0
CD A:GLU90 5.0 11.8 1.0

Calcium binding site 5 out of 11 in 6wyf

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Calcium binding site 5 out of 11 in the Crystal Structure of Human H-Chain Ferritin Variant 157C Delta C-Star Modified with A Raft Agent Soaked in An Acrylate Solution


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Crystal Structure of Human H-Chain Ferritin Variant 157C Delta C-Star Modified with A Raft Agent Soaked in An Acrylate Solution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca206

b:9.6
occ:0.21
 O A:HOH443 2.3 12.2 1.0
O A:HOH414 2.4 15.1 1.0
O A:HOH337 2.4 11.9 1.0
CA A:CA205 3.5 13.0 0.2
O A:HOH493 3.7 14.2 1.0
CA A:CA208 3.8 10.5 0.4
O A:ASP89 3.9 11.9 1.0
O A:HOH608 4.2 19.2 1.0
O A:HOH420 4.3 23.0 1.0
OE1 A:GLU90 4.3 12.2 1.0
O A:HOH568 4.5 20.1 1.0
OE2 A:GLU90 4.5 13.4 1.0
CD A:GLU90 4.7 11.8 1.0
HA A:GLU90 4.9 9.6 1.0

Calcium binding site 6 out of 11 in 6wyf

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Calcium binding site 6 out of 11 in the Crystal Structure of Human H-Chain Ferritin Variant 157C Delta C-Star Modified with A Raft Agent Soaked in An Acrylate Solution


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Crystal Structure of Human H-Chain Ferritin Variant 157C Delta C-Star Modified with A Raft Agent Soaked in An Acrylate Solution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca207

b:18.1
occ:0.75
 H A:TYR12 2.4 11.8 1.0
O A:HOH526 2.7 46.6 1.0
HG2 A:ARG9 2.8 14.3 1.0
H A:ASN11 3.1 12.3 1.0
HE A:ARG9 3.1 18.4 1.0
O A:HOH541 3.1 34.8 1.0
HD3 A:ARG9 3.2 20.0 1.0
N A:TYR12 3.3 9.9 1.0
O A:HOH505 3.3 46.2 1.0
N A:ASN11 3.4 10.3 1.0
O A:TYR12 3.5 11.7 1.0
HA A:GLN10 3.5 11.9 1.0
CG A:ARG9 3.6 12.0 1.0
CD A:ARG9 3.7 16.7 1.0
NE A:ARG9 3.7 15.4 1.0
HB3 A:TYR12 3.8 11.8 1.0
O A:HOH475 3.8 25.0 1.0
C A:GLN10 3.9 9.6 1.0
CA A:GLN10 4.0 9.9 1.0
N A:GLN10 4.0 9.1 1.0
HA A:ASN11 4.0 12.1 1.0
C A:TYR12 4.1 9.7 1.0
O A:HOH558 4.1 41.2 1.0
CA A:TYR12 4.1 9.8 1.0
CA A:ASN11 4.1 10.1 1.0
C A:ASN11 4.2 9.8 1.0
H A:GLN10 4.2 10.9 1.0
HG3 A:ARG9 4.3 14.3 1.0
HB3 A:ARG9 4.3 14.2 1.0
C A:ARG9 4.3 10.5 1.0
CB A:TYR12 4.4 9.9 1.0
O A:ARG9 4.5 12.4 1.0
CB A:ARG9 4.5 11.8 1.0
HB2 A:TYR12 4.6 11.8 1.0
HD2 A:ARG9 4.6 20.0 1.0
O A:HOH585 4.6 35.1 1.0
O A:GLN10 4.7 9.4 1.0
CZ A:ARG9 4.9 13.6 1.0
HH21 A:ARG9 5.0 15.8 1.0
CA A:ARG9 5.0 10.4 1.0

Calcium binding site 7 out of 11 in 6wyf

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Calcium binding site 7 out of 11 in the Crystal Structure of Human H-Chain Ferritin Variant 157C Delta C-Star Modified with A Raft Agent Soaked in An Acrylate Solution


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Crystal Structure of Human H-Chain Ferritin Variant 157C Delta C-Star Modified with A Raft Agent Soaked in An Acrylate Solution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca208

b:10.5
occ:0.38
 O A:HOH464 2.4 14.4 1.0
O A:HOH493 2.5 14.2 1.0
O A:HOH337 2.5 11.9 1.0
O A:HOH413 2.5 15.8 1.0
HA A:ASP89 3.8 10.9 1.0
CA A:CA206 3.8 9.6 0.2
HE3 A:LYS87 4.3 20.1 1.0
O A:ASP89 4.3 11.9 1.0
O A:HOH443 4.4 12.2 1.0
CA A:ASP89 4.7 9.1 1.0
O A:HOH416 4.7 13.3 1.0
HE2 A:LYS87 4.7 20.1 1.0
O A:HOH568 4.7 20.1 1.0
C A:ASP89 4.8 9.6 1.0
OD1 A:ASP89 4.8 12.8 1.0
O A:HOH435 4.9 15.6 1.0
O A:HOH419 4.9 16.8 1.0
O A:PRO88 4.9 8.6 1.0
CE A:LYS87 5.0 16.8 1.0

Calcium binding site 8 out of 11 in 6wyf

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Calcium binding site 8 out of 11 in the Crystal Structure of Human H-Chain Ferritin Variant 157C Delta C-Star Modified with A Raft Agent Soaked in An Acrylate Solution


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Crystal Structure of Human H-Chain Ferritin Variant 157C Delta C-Star Modified with A Raft Agent Soaked in An Acrylate Solution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca209

b:20.7
occ:0.59
 O A:HOH512 2.4 17.6 1.0
HD22 A:ASN21 2.5 11.2 1.0
HA A:ALA18 2.7 11.4 1.0
O A:HOH329 3.0 19.6 1.0
O A:HOH415 3.2 14.1 1.0
HG2 A:GLU17 3.3 12.1 1.0
ND2 A:ASN21 3.3 9.3 1.0
HB2 A:ALA18 3.3 12.9 1.0
CA A:ALA18 3.5 9.5 1.0
HD21 A:ASN21 3.5 11.2 1.0
CB A:ALA18 3.8 10.7 1.0
N A:ALA18 3.8 9.2 1.0
HD2 A:PHE81 3.8 15.1 1.0
HB1 A:ALA18 4.0 12.9 1.0
HB2 A:ASN21 4.0 9.5 1.0
H A:ALA18 4.2 11.0 1.0
CG A:GLU17 4.2 10.1 1.0
C A:GLU17 4.2 8.3 1.0
O A:GLU17 4.2 8.8 1.0
O A:HOH624 4.3 53.8 1.0
O A:HOH304 4.4 20.7 1.0
CG A:ASN21 4.4 8.4 1.0
O A:HOH427 4.6 27.1 1.0
CD A:GLU17 4.6 11.0 1.0
HB3 A:GLU17 4.6 11.2 1.0
CD2 A:PHE81 4.6 12.6 1.0
HB2 A:PHE81 4.6 11.7 1.0
O A:HOH492 4.6 44.9 1.0
CB A:ASN21 4.7 7.9 1.0
HB3 A:ALA18 4.7 12.9 1.0
OE2 A:GLU17 4.7 11.6 1.0
C A:ALA18 4.8 9.1 1.0
HG3 A:GLU17 4.8 12.1 1.0
O A:HOH563 4.8 29.1 1.0
CB A:GLU17 4.9 9.4 1.0
O A:ARG79 4.9 9.9 1.0
HB3 A:ASN21 5.0 9.5 1.0
O A:ALA18 5.0 9.6 1.0

Calcium binding site 9 out of 11 in 6wyf

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Calcium binding site 9 out of 11 in the Crystal Structure of Human H-Chain Ferritin Variant 157C Delta C-Star Modified with A Raft Agent Soaked in An Acrylate Solution


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 9 of Crystal Structure of Human H-Chain Ferritin Variant 157C Delta C-Star Modified with A Raft Agent Soaked in An Acrylate Solution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca210

b:25.6
occ:0.33
 O A:HOH322 1.9 22.0 0.3
OE2 A:GLU134 2.1 20.4 0.4
OE1 A:GLU134 2.3 22.4 0.6
OD1 A:ASP131 2.7 25.6 1.0
CD A:GLU134 3.1 22.8 0.4
O A:HOH364 3.5 13.8 1.0
HG3 A:GLU134 3.5 25.7 0.4
CD A:GLU134 3.5 22.0 0.6
CG A:ASP131 3.8 21.8 1.0
CG A:GLU134 3.8 21.4 0.4
OE1 A:GLU134 3.9 22.9 0.4
OE2 A:GLU134 4.0 23.3 0.6
HA A:ASP131 4.1 16.9 1.0
HG2 A:GLU134 4.2 25.7 0.4
HB2 A:ASP131 4.3 21.1 1.0
HB2 A:GLU134 4.3 25.1 0.6
CB A:ASP131 4.5 17.6 1.0
HB3 A:GLU134 4.5 25.1 0.6
OD2 A:ASP131 4.6 22.7 1.0
CG A:GLU134 4.7 20.1 0.6
CB A:GLU134 4.8 20.9 0.6
CA A:ASP131 4.8 14.1 1.0

Calcium binding site 10 out of 11 in 6wyf

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Calcium binding site 10 out of 11 in the Crystal Structure of Human H-Chain Ferritin Variant 157C Delta C-Star Modified with A Raft Agent Soaked in An Acrylate Solution


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 10 of Crystal Structure of Human H-Chain Ferritin Variant 157C Delta C-Star Modified with A Raft Agent Soaked in An Acrylate Solution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca211

b:31.6
occ:0.68
 O A:HOH533 2.7 22.4 1.0
HG3 A:GLN83 2.9 15.1 1.0
HA A:ARG22 3.2 9.9 0.7
HA A:ARG22 3.2 11.2 0.3
HB3 A:ASN25 3.3 9.9 1.0
HG2 A:ARG22 3.4 16.1 0.7
HB2 A:ASN25 3.4 9.9 1.0
HB2 A:GLN83 3.5 12.2 1.0
HG3 A:ARG22 3.6 19.2 0.3
CB A:ASN25 3.7 8.3 1.0
CG A:GLN83 3.7 12.6 1.0
O A:HOH392 3.8 25.1 1.0
HG2 A:GLN83 3.8 15.1 1.0
CG A:ASN25 3.9 7.8 1.0
CB A:GLN83 4.0 10.2 1.0
OD1 A:ASN25 4.0 9.4 1.0
CA A:ARG22 4.1 8.3 0.7
CA A:ARG22 4.1 9.4 0.3
HB3 A:GLN83 4.2 12.2 1.0
CG A:ARG22 4.3 13.5 0.7
CG A:ARG22 4.5 16.0 0.3
HB2 A:ARG22 4.5 15.1 0.3
HB3 A:ARG22 4.5 12.0 0.7
CB A:ARG22 4.6 10.0 0.7
ND2 A:ASN25 4.6 8.9 1.0
CB A:ARG22 4.6 12.6 0.3
O A:ASN21 4.7 8.5 1.0
O A:ARG22 4.7 8.7 1.0
HG3 A:ARG22 4.8 16.1 0.7
HD22 A:ASN25 4.8 10.6 1.0
HG2 A:ARG22 4.9 19.2 0.3
O A:HOH403 4.9 14.1 1.0
N A:ARG22 4.9 8.3 1.0
C A:ARG22 4.9 7.7 1.0
HD2 A:ARG22 5.0 20.4 0.7

Reference:

K.Han, J.B.Bailey, L.Zhang, F.A.Tezcan. Anisotropic Dynamics and Mechanics of Macromolecular Crystals Containing Lattice-Patterned Polymer Networks. J.Am.Chem.Soc. V. 142 19402 2020.
ISSN: ESSN 1520-5126
PubMed: 33124805
DOI: 10.1021/JACS.0C10065
Page generated: Tue Jul 16 17:36:19 2024

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