Atomistry » Calcium » PDB 6wm1-6x68 » 6wyf
Atomistry »
  Calcium »
    PDB 6wm1-6x68 »
      6wyf »

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

Go back to Calcium Binding Sites List in 6wyf
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


Mono view


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

Go back to Calcium Binding Sites List in 6wyf
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


Mono view


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

Go back to Calcium Binding Sites List in 6wyf
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

Go back to Calcium Binding Sites List in 6wyf
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

Go back to Calcium Binding Sites List in 6wyf
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

Go back to Calcium Binding Sites List in 6wyf
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

Go back to Calcium Binding Sites List in 6wyf
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

Go back to Calcium Binding Sites List in 6wyf
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

Go back to Calcium Binding Sites List in 6wyf
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

Go back to Calcium Binding Sites List in 6wyf
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

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy