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Calcium in PDB 6wyg: Crystal Structure of Human H-Chain Ferritin Variant 157C Delta C-Star Modified with A Raft Agent

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

All present enzymatic activity of Crystal Structure of Human H-Chain Ferritin Variant 157C Delta C-Star Modified with A Raft Agent:
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, PDB code: 6wyg 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) 50.07 / 2.27
Space group H 3 2
Cell size a, b, c (Å), α, β, γ (°) 126.810, 126.810, 281.285, 90.00, 90.00, 120.00
R / Rfree (%) 19.8 / 26

Other elements in 6wyg:

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

Iron (Fe) 9 atoms

Calcium 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 (pdb code 6wyg). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 8 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, PDB code: 6wyg:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Calcium binding site 1 out of 8 in 6wyg

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Calcium binding site 1 out of 8 in the Crystal Structure of Human H-Chain Ferritin Variant 157C Delta C-Star Modified with A Raft Agent


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca204

b:0.4
occ:1.00
 OE1 A:GLN112 2.3 76.9 1.0
O A:HOH354 2.5 49.5 1.0
OD1 A:ASN109 2.5 78.9 1.0
CD A:GLN112 3.3 74.3 1.0
NE2 A:GLN112 3.6 80.3 1.0
CG A:ASN109 3.7 73.5 1.0
ND2 A:ASN109 4.5 71.0 1.0
CG A:GLN112 4.7 56.2 1.0
CB A:ASN109 4.8 58.8 1.0
CA A:ASN109 4.9 56.7 1.0
CB A:GLN112 5.0 51.2 1.0

Calcium binding site 2 out of 8 in 6wyg

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Calcium binding site 2 out of 8 in the Crystal Structure of Human H-Chain Ferritin Variant 157C Delta C-Star Modified with A Raft Agent


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca203

b:65.0
occ:1.00
 OD2 B:ASP84 2.4 62.4 1.0
OD1 B:ASP84 2.9 51.2 1.0
CG B:ASP84 3.0 61.6 1.0
CB B:ASP84 4.6 50.9 1.0

Calcium binding site 3 out of 8 in 6wyg

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Calcium binding site 3 out of 8 in the Crystal Structure of Human H-Chain Ferritin Variant 157C Delta C-Star Modified with A Raft Agent


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca204

b:98.9
occ:1.00
 O B:HOH368 2.8 66.5 1.0
O B:HOH376 2.9 58.7 1.0
OE1 B:GLU147 2.9 61.0 1.0
O B:HOH312 3.0 64.8 1.0
OE2 B:GLU147 3.3 61.3 1.0
CD B:GLU147 3.5 49.5 1.0
O B:HOH318 3.7 60.7 1.0
NE2 B:GLN58 4.5 59.4 1.0
CG B:GLU147 5.0 41.3 1.0

Calcium binding site 4 out of 8 in 6wyg

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Calcium binding site 4 out of 8 in the Crystal Structure of Human H-Chain Ferritin Variant 157C Delta C-Star Modified with A Raft Agent


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca203

b:53.0
occ:1.00
 OE2 C:GLU134 2.1 71.2 1.0
OD1 C:ASP131 2.8 52.7 1.0
CD C:GLU134 3.3 67.3 1.0
CG C:ASP131 3.9 56.4 1.0
CA C:CA204 3.9 83.5 1.0
OE1 C:GLU134 4.0 73.3 1.0
O C:HOH315 4.3 51.6 1.0
CB C:ASP131 4.3 55.6 1.0
CB C:GLU134 4.5 51.0 1.0
CG C:GLU134 4.5 61.3 1.0
CA C:ASP131 4.6 53.4 1.0
OD2 C:ASP131 4.9 66.7 1.0

Calcium binding site 5 out of 8 in 6wyg

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Calcium binding site 5 out of 8 in the Crystal Structure of Human H-Chain Ferritin Variant 157C Delta C-Star Modified with A Raft Agent


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca204

b:83.5
occ:1.00
 O C:HOH315 3.1 51.6 1.0
OE1 C:GLU134 3.8 73.3 1.0
CA C:CA203 3.9 53.0 1.0
OE2 C:GLU134 4.2 71.2 1.0
CD C:GLU134 4.4 67.3 1.0

Calcium binding site 6 out of 8 in 6wyg

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Calcium binding site 6 out of 8 in the Crystal Structure of Human H-Chain Ferritin Variant 157C Delta C-Star Modified with A Raft Agent


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca203

b:68.2
occ:0.33
 OE1 D:GLU134 2.5 71.2 1.0
OD1 D:ASP131 2.6 79.7 1.0
CD D:GLU134 3.6 72.4 1.0
CG D:ASP131 3.7 75.4 1.0
CA D:CA204 4.1 0.6 0.3
OE2 D:GLU134 4.2 75.5 1.0
CB D:ASP131 4.2 69.9 1.0
CA D:ASP131 4.7 65.7 1.0
OD2 D:ASP131 4.7 69.0 1.0
CB D:GLU134 4.7 71.5 1.0
CG D:GLU134 4.8 71.9 1.0

Calcium binding site 7 out of 8 in 6wyg

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Calcium binding site 7 out of 8 in the Crystal Structure of Human H-Chain Ferritin Variant 157C Delta C-Star Modified with A Raft Agent


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca204

b:0.6
occ:0.33
 OE2 D:GLU134 2.9 75.5 1.0
CD D:GLU134 3.7 72.4 1.0
OE1 D:GLU134 3.8 71.2 1.0
CA D:CA203 4.1 68.2 0.3

Calcium binding site 8 out of 8 in 6wyg

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


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca205

b:47.4
occ:0.50
 OE2 D:GLU90 2.7 87.2 1.0
CD D:GLU90 3.0 87.2 1.0
OE1 D:GLU90 3.1 86.4 1.0
CG D:GLU90 4.2 83.2 1.0

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 17:36:22 2024

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