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Calcium in PDB 1x8k: Crystal Structure of Retinol Dehydratase in Complex with Anhydroretinol and Inactive Cofactor Pap

Protein crystallography data

The structure of Crystal Structure of Retinol Dehydratase in Complex with Anhydroretinol and Inactive Cofactor Pap, PDB code: 1x8k was solved by S.Pakhomova, J.Buck, M.E.Newcomer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 15.00 / 2.75
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 81.286, 66.661, 84.464, 90.00, 110.66, 90.00
R / Rfree (%) 19.4 / 25.5

Other elements in 1x8k:

The structure of Crystal Structure of Retinol Dehydratase in Complex with Anhydroretinol and Inactive Cofactor Pap also contains other interesting chemical elements:

Mercury (Hg) 2 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Retinol Dehydratase in Complex with Anhydroretinol and Inactive Cofactor Pap (pdb code 1x8k). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Crystal Structure of Retinol Dehydratase in Complex with Anhydroretinol and Inactive Cofactor Pap, PDB code: 1x8k:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in 1x8k

Go back to Calcium Binding Sites List in 1x8k
Calcium binding site 1 out of 2 in the Crystal Structure of Retinol Dehydratase in Complex with Anhydroretinol and Inactive Cofactor Pap


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 Retinol Dehydratase in Complex with Anhydroretinol and Inactive Cofactor Pap within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1104

b:55.1
occ:1.00
OD1 A:ASN121 2.3 17.2 1.0
OD1 A:ASP122 2.4 18.3 1.0
O A:GLU118 2.7 16.3 1.0
CG A:ASN121 3.4 17.3 1.0
CG A:ASP122 3.4 18.2 1.0
OD2 A:ASP122 3.8 17.9 1.0
C A:GLU118 3.9 16.1 1.0
ND2 A:ASN121 4.0 18.1 1.0
N A:ASP122 4.4 18.2 1.0
CA A:GLU118 4.6 15.8 1.0
CB A:ASN121 4.6 17.4 1.0
CB A:ASP122 4.7 18.6 1.0
C A:ASN121 4.8 17.7 1.0
N A:ASN121 4.8 16.8 1.0
CA A:ASP122 4.9 18.7 1.0
N A:GLU119 4.9 16.5 1.0
CA A:ASN121 4.9 17.3 1.0

Calcium binding site 2 out of 2 in 1x8k

Go back to Calcium Binding Sites List in 1x8k
Calcium binding site 2 out of 2 in the Crystal Structure of Retinol Dehydratase in Complex with Anhydroretinol and Inactive Cofactor Pap


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 Retinol Dehydratase in Complex with Anhydroretinol and Inactive Cofactor Pap within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca2204

b:33.5
occ:1.00
O B:GLU118 2.5 15.1 1.0
OD1 B:ASN121 2.6 17.6 1.0
OD1 B:ASP122 2.6 17.6 1.0
CG B:ASN121 3.4 16.9 1.0
C B:GLU118 3.6 15.1 1.0
CG B:ASP122 3.6 17.5 1.0
ND2 B:ASN121 3.8 17.1 1.0
OD2 B:ASP122 4.0 16.7 1.0
CA B:GLU118 4.3 15.0 1.0
N B:ASP122 4.4 17.3 1.0
CB B:GLU118 4.7 14.7 1.0
CB B:ASN121 4.7 16.4 1.0
N B:GLU119 4.7 15.3 1.0
N B:ASN121 4.8 15.9 1.0
C B:ASN121 4.9 16.8 1.0
CB B:ASP122 4.9 17.7 1.0
CA B:ASN121 4.9 16.3 1.0
CA B:GLU119 5.0 15.4 1.0

Reference:

S.Pakhomova, J.Buck, M.E.Newcomer. The Structures of the Unique Sulfotransferase Retinol Dehydratase with Product and Inhibitors Provide Insight Into Enzyme Mechanism and Inhibition. Protein Sci. V. 14 176 2005.
ISSN: ISSN 0961-8368
PubMed: 15608121
DOI: 10.1110/PS.041061105
Page generated: Sat Dec 12 03:26:39 2020

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