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Cadmium in PDB 8h8l: Crystal Structure of Apo-R52F/E56F/R59F/E63F-Rhlfr

Protein crystallography data

The structure of Crystal Structure of Apo-R52F/E56F/R59F/E63F-Rhlfr, PDB code: 8h8l was solved by Y.Hishikawa, H.Noya, B.Maity, S.Abe, T.Ueno, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.28 / 1.50
Space group F 4 3 2
Cell size a, b, c (Å), α, β, γ (°) 181.31, 181.31, 181.31, 90, 90, 90
R / Rfree (%) 15.6 / 17.1

Other elements in 8h8l:

The structure of Crystal Structure of Apo-R52F/E56F/R59F/E63F-Rhlfr also contains other interesting chemical elements:

Chlorine (Cl) 1 atom

Cadmium Binding Sites:

The binding sites of Cadmium atom in the Crystal Structure of Apo-R52F/E56F/R59F/E63F-Rhlfr (pdb code 8h8l). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 10 binding sites of Cadmium where determined in the Crystal Structure of Apo-R52F/E56F/R59F/E63F-Rhlfr, PDB code: 8h8l:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Cadmium binding site 1 out of 10 in 8h8l

Go back to Cadmium Binding Sites List in 8h8l
Cadmium binding site 1 out of 10 in the Crystal Structure of Apo-R52F/E56F/R59F/E63F-Rhlfr


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of Crystal Structure of Apo-R52F/E56F/R59F/E63F-Rhlfr within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd202

b:7.3
occ:0.50
 OD1 A:ASP80 2.3 6.4 1.0
OD2 A:ASP80 2.4 9.2 1.0
CL A:CL213 2.4 15.3 1.0
CG A:ASP80 2.7 7.3 1.0
CB A:ASP80 4.2 7.0 1.0
O A:HOH390 4.4 12.4 1.0
O A:HOH325 4.8 12.4 1.0

Cadmium binding site 2 out of 10 in 8h8l

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Cadmium binding site 2 out of 10 in the Crystal Structure of Apo-R52F/E56F/R59F/E63F-Rhlfr


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of Crystal Structure of Apo-R52F/E56F/R59F/E63F-Rhlfr within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd203

b:23.2
occ:0.20
 O A:HOH312 2.1 28.6 1.0
O A:HOH301 2.3 29.4 1.0
OD1 A:ASP127 3.5 22.7 1.0
OG A:SER131 4.1 21.3 1.0
CD A:CD204 4.1 22.7 0.1
OE1 A:GLU130 4.3 21.0 1.0
CG A:ASP127 4.7 17.5 1.0

Cadmium binding site 3 out of 10 in 8h8l

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Cadmium binding site 3 out of 10 in the Crystal Structure of Apo-R52F/E56F/R59F/E63F-Rhlfr


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 3 of Crystal Structure of Apo-R52F/E56F/R59F/E63F-Rhlfr within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd204

b:22.7
occ:0.10
 CD A:CD205 1.6 14.9 0.2
OE1 A:GLU130 2.4 21.0 1.0
CD A:CD210 2.8 28.5 0.1
CD A:GLU130 3.4 16.8 1.0
O A:HOH301 3.4 29.4 1.0
OE2 A:GLU130 3.8 10.4 1.0
CD A:CD203 4.1 23.2 0.2
CG A:GLU130 4.7 15.3 1.0

Cadmium binding site 4 out of 10 in 8h8l

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Cadmium binding site 4 out of 10 in the Crystal Structure of Apo-R52F/E56F/R59F/E63F-Rhlfr


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 4 of Crystal Structure of Apo-R52F/E56F/R59F/E63F-Rhlfr within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd205

b:14.9
occ:0.25
 CD A:CD204 1.6 22.7 0.1
CD A:CD210 1.8 28.5 0.1
OE1 A:GLU130 2.5 21.0 1.0
CD A:GLU130 3.0 16.8 1.0
OE2 A:GLU130 3.0 10.4 1.0
CG A:GLU130 4.3 15.3 1.0
CD A:CD206 4.5 37.0 0.2
O A:HOH301 4.7 29.4 1.0
O A:HOH510 4.7 27.9 1.0
CB A:GLU130 4.9 13.6 1.0

Cadmium binding site 5 out of 10 in 8h8l

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Cadmium binding site 5 out of 10 in the Crystal Structure of Apo-R52F/E56F/R59F/E63F-Rhlfr


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 5 of Crystal Structure of Apo-R52F/E56F/R59F/E63F-Rhlfr within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd206

b:37.0
occ:0.20
 CD A:CD210 2.7 28.5 0.1
CE1 A:HIS114 2.9 9.1 1.0
NE2 A:HIS114 3.2 9.3 1.0
O A:HOH510 3.3 27.9 1.0
OE2 A:GLU130 3.3 10.4 1.0
CB A:CYS126 3.7 11.7 1.0
OG A:SER118 3.9 12.1 0.5
SG A:CYS126 4.0 12.8 1.0
ND1 A:HIS114 4.1 10.8 1.0
CD A:CD205 4.5 14.9 0.2
CD A:GLU130 4.5 16.8 1.0
CD2 A:HIS114 4.5 9.3 1.0
OG A:SER118 4.8 10.9 0.5
CB A:SER118 4.9 10.6 0.5
CA A:CYS126 5.0 10.4 1.0
CG A:HIS114 5.0 8.9 1.0

Cadmium binding site 6 out of 10 in 8h8l

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Cadmium binding site 6 out of 10 in the Crystal Structure of Apo-R52F/E56F/R59F/E63F-Rhlfr


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 6 of Crystal Structure of Apo-R52F/E56F/R59F/E63F-Rhlfr within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd207

b:30.4
occ:0.20
 OE2 A:GLU11 2.4 13.0 1.0
OE1 A:GLU11 2.6 17.4 1.0
O A:HOH433 2.8 20.5 1.0
CD A:GLU11 2.9 14.4 1.0
O A:HOH505 3.5 38.3 1.0
OG1 A:THR10 3.9 15.1 1.0
CG A:GLU11 4.4 11.1 1.0
CB A:SER9 4.5 8.2 1.0
OE1 A:GLN120 4.6 20.1 1.0
N A:THR10 4.7 8.8 1.0
NE2 A:GLN120 4.8 20.1 1.0
N A:GLU11 4.9 8.4 1.0
O A:HOH317 5.0 42.3 1.0

Cadmium binding site 7 out of 10 in 8h8l

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Cadmium binding site 7 out of 10 in the Crystal Structure of Apo-R52F/E56F/R59F/E63F-Rhlfr


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 7 of Crystal Structure of Apo-R52F/E56F/R59F/E63F-Rhlfr within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd208

b:35.5
occ:0.20
 NE2 A:HIS49 2.2 20.7 1.0
CE1 A:HIS49 2.8 20.4 1.0
CD2 A:HIS49 3.4 20.0 1.0
CG A:GLU45 3.9 13.4 1.0
OE1 A:GLU45 4.0 27.1 1.0
CD A:GLU45 4.0 18.7 1.0
ND1 A:HIS49 4.1 24.1 1.0
O A:HOH335 4.2 20.6 1.0
CG A:HIS49 4.4 16.6 1.0
O A:HOH446 4.5 39.7 1.0
OE2 A:GLU45 4.7 20.5 1.0
CD A:CD209 4.7 31.6 0.1

Cadmium binding site 8 out of 10 in 8h8l

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Cadmium binding site 8 out of 10 in the Crystal Structure of Apo-R52F/E56F/R59F/E63F-Rhlfr


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 8 of Crystal Structure of Apo-R52F/E56F/R59F/E63F-Rhlfr within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd209

b:31.6
occ:0.15
 OE2 A:GLU45 2.4 20.5 1.0
OE1 A:GLU45 3.0 27.1 1.0
CD A:GLU45 3.0 18.7 1.0
O A:HOH446 3.8 39.7 1.0
CG A:GLU45 4.4 13.4 1.0
O A:HOH347 4.5 17.5 1.0
CA A:ASP174 4.6 40.1 1.0
N A:ASP174 4.7 37.4 1.0
CD A:CD208 4.7 35.5 0.2

Cadmium binding site 9 out of 10 in 8h8l

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Cadmium binding site 9 out of 10 in the Crystal Structure of Apo-R52F/E56F/R59F/E63F-Rhlfr


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 9 of Crystal Structure of Apo-R52F/E56F/R59F/E63F-Rhlfr within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd210

b:28.5
occ:0.15
 CD A:CD205 1.8 14.9 0.2
OE2 A:GLU130 2.5 10.4 1.0
CD A:CD206 2.7 37.0 0.2
CD A:CD204 2.8 22.7 0.1
CD A:GLU130 3.1 16.8 1.0
OE1 A:GLU130 3.2 21.0 1.0
O A:HOH510 3.6 27.9 1.0
NE2 A:HIS114 4.3 9.3 1.0
CG A:GLU130 4.6 15.3 1.0
CE1 A:HIS114 4.6 9.1 1.0

Cadmium binding site 10 out of 10 in 8h8l

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Cadmium binding site 10 out of 10 in the Crystal Structure of Apo-R52F/E56F/R59F/E63F-Rhlfr


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 10 of Crystal Structure of Apo-R52F/E56F/R59F/E63F-Rhlfr within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd211

b:29.1
occ:0.25
 NE2 A:HIS132 2.2 22.5 1.0
CE1 A:HIS132 2.8 23.3 1.0
CD2 A:HIS132 3.4 19.5 1.0
ND1 A:HIS132 4.0 20.2 1.0
NH2 A:ARG64 4.2 18.3 0.5
CG A:HIS132 4.3 18.0 1.0

Reference:

Y.Hishikawa, H.Noya, S.Nagatoishi, T.Yoshidome, B.Maity, K.Tsumoto, S.Abe, T.Ueno. Elucidating Conformational Dynamics and Thermostability of Designed Aromatic Clusters By Using Protein Cages. Chemistry V. 29 00488 2023.
ISSN: ISSN 0947-6539
PubMed: 37070368
DOI: 10.1002/CHEM.202300488
Page generated: Fri Jul 19 20:27:32 2024

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