Cobalt in PDB 2amx: Crystal Structure of Plasmodium Yoelii Adenosine Deaminase (PY02076)

All present enzymatic activity of Crystal Structure of Plasmodium Yoelii Adenosine Deaminase (PY02076):
3.5.4.4;

The structure of Crystal Structure of Plasmodium Yoelii Adenosine Deaminase (PY02076), PDB code: 2amx was solved by A.Dong, M.Vedadi, G.Wasney, Y.Zhao, J.Lew, Z.Alam, M.Melone, I.Koeieradzki, A.M.Edwards, C.H.Arrowsmith, J.Weigelt, M.Sundstrom, A.Bochkarev, R.Hui, M.Amani, Structural Genomicsconsortium (Sgc), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	42.90 / 2.02
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	66.719, 90.332, 137.086, 90.00, 90.00, 90.00
R / Rfree (%)	19.6 / 24.6

The binding sites of Cobalt atom in the Crystal Structure of Plasmodium Yoelii Adenosine Deaminase (PY02076) (pdb code 2amx). This binding sites where shown within 5.0 Angstroms radius around Cobalt atom.
In total 5 binding sites of Cobalt where determined in the Crystal Structure of Plasmodium Yoelii Adenosine Deaminase (PY02076), PDB code: 2amx:
Jump to Cobalt binding site number: 1; 2; 3; 4; 5;

Cobalt binding site 1 out of 5 in the Crystal Structure of Plasmodium Yoelii Adenosine Deaminase (PY02076)


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 1 of Crystal Structure of Plasmodium Yoelii Adenosine Deaminase (PY02076) within 5.0Å range: probe atom residue distance (Å) B Occ A:Co1000 b:24.6 occ:1.00 NE2 A:HIS57 2.0 20.9 1.0 NE2 A:HIS55 2.2 18.2 1.0 NE2 A:HIS239 2.3 15.5 1.0 OD1 A:ASP323 2.3 15.6 1.0 CD2 A:HIS57 2.9 19.5 1.0 CE1 A:HIS57 3.1 18.4 1.0 CD2 A:HIS55 3.1 17.6 1.0 CE1 A:HIS55 3.2 18.7 1.0 CD2 A:HIS239 3.2 16.5 1.0 CG A:ASP323 3.2 20.3 1.0 CE1 A:HIS239 3.3 19.7 1.0 OD2 A:ASP323 3.5 20.3 1.0 NE2 A:HIS266 3.9 21.9 1.0 O A:HOH2095 4.0 31.1 1.0 CG A:HIS57 4.1 18.1 1.0 ND1 A:HIS57 4.2 19.6 1.0 ND1 A:HIS55 4.3 20.7 1.0 CG A:HIS55 4.3 16.1 1.0 CG A:HIS239 4.3 17.8 1.0 ND1 A:HIS239 4.4 18.6 1.0 CB A:ASP323 4.6 18.9 1.0 CE1 A:HIS266 4.7 20.1 1.0 CD2 A:HIS266 4.8 23.1 1.0 OD2 A:ASP324 4.9 24.7 1.0 CA A:ASP323 4.9 19.1 1.0

Cobalt binding site 2 out of 5 in the Crystal Structure of Plasmodium Yoelii Adenosine Deaminase (PY02076)


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 2 of Crystal Structure of Plasmodium Yoelii Adenosine Deaminase (PY02076) within 5.0Å range: probe atom residue distance (Å) B Occ A:Co1002 b:84.6 occ:1.00 OE1 A:GLU370 2.5 43.8 1.0 NE2 A:HIS177 2.6 31.9 1.0 OE2 A:GLU370 2.8 42.9 1.0 CD A:GLU370 3.0 41.7 1.0 CD2 A:HIS177 3.4 28.4 1.0 CE1 A:HIS177 3.7 27.2 1.0 CG A:GLU370 4.5 35.5 1.0 CG A:HIS177 4.7 27.8 1.0 CB A:ASN174 4.7 32.4 1.0 ND1 A:HIS177 4.7 32.2 1.0

Cobalt binding site 3 out of 5 in the Crystal Structure of Plasmodium Yoelii Adenosine Deaminase (PY02076)


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 3 of Crystal Structure of Plasmodium Yoelii Adenosine Deaminase (PY02076) within 5.0Å range: probe atom residue distance (Å) B Occ B:Co1000 b:23.2 occ:1.00 NE2 B:HIS57 2.1 19.3 1.0 NE2 B:HIS55 2.1 14.7 1.0 NE2 B:HIS239 2.3 16.8 1.0 OD1 B:ASP323 2.4 20.4 1.0 CD2 B:HIS57 3.0 19.4 1.0 CD2 B:HIS55 3.1 14.7 1.0 CE1 B:HIS57 3.1 18.9 1.0 CE1 B:HIS55 3.2 14.7 1.0 CD2 B:HIS239 3.2 17.3 1.0 CE1 B:HIS239 3.3 17.1 1.0 CG B:ASP323 3.4 19.6 1.0 OD2 B:ASP323 3.6 20.6 1.0 NE2 B:HIS266 3.8 23.0 1.0 UNK B:UNX2005 4.1 0.0 1.0 CG B:HIS57 4.2 17.2 1.0 ND1 B:HIS57 4.2 17.0 1.0 CG B:HIS55 4.2 14.9 1.0 ND1 B:HIS55 4.2 13.9 1.0 CG B:HIS239 4.4 20.9 1.0 ND1 B:HIS239 4.4 18.8 1.0 CD2 B:HIS266 4.6 22.9 1.0 CE1 B:HIS266 4.7 23.4 1.0 CB B:ASP323 4.7 16.8 1.0 CA B:ASP323 5.0 17.1 1.0

Cobalt binding site 4 out of 5 in the Crystal Structure of Plasmodium Yoelii Adenosine Deaminase (PY02076)


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 4 of Crystal Structure of Plasmodium Yoelii Adenosine Deaminase (PY02076) within 5.0Å range: probe atom residue distance (Å) B Occ B:Co1001 b:44.6 occ:1.00 NE2 B:HIS222 2.2 36.2 1.0 NE2 B:HIS212 2.2 30.6 1.0 O B:HOH2177 2.4 26.5 1.0 O B:HOH2205 2.5 43.2 1.0 CE1 B:HIS212 3.0 30.6 1.0 CD2 B:HIS222 3.1 36.5 1.0 CD2 B:LEU219 3.2 45.5 1.0 CE1 B:HIS222 3.2 36.3 1.0 CD2 B:HIS212 3.3 24.9 1.0 ND1 B:HIS212 4.2 28.0 1.0 CG B:HIS222 4.3 37.5 1.0 ND1 B:HIS222 4.3 37.6 1.0 CG B:HIS212 4.3 25.5 1.0 O B:ARG215 4.5 45.5 1.0 O B:ASP218 4.5 47.5 1.0 CD1 B:ILE217 4.6 52.0 1.0 CG B:LEU219 4.7 44.4 1.0

Cobalt binding site 5 out of 5 in the Crystal Structure of Plasmodium Yoelii Adenosine Deaminase (PY02076)


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 5 of Crystal Structure of Plasmodium Yoelii Adenosine Deaminase (PY02076) within 5.0Å range: probe atom residue distance (Å) B Occ B:Co1002 b:68.1 occ:1.00 OD1 B:ASN174 2.5 42.5 1.0 NE2 B:HIS177 2.5 30.7 1.0 OE1 B:GLU370 2.5 37.4 1.0 OE2 B:GLU370 2.6 40.7 1.0 CD B:GLU370 2.9 36.3 1.0 CG B:ASN174 3.2 36.9 1.0 ND2 B:ASN174 3.3 38.4 1.0 CD2 B:HIS177 3.4 27.9 1.0 CE1 B:HIS177 3.5 30.1 1.0 O B:HOH2234 3.6 43.1 1.0 CG B:GLU370 4.4 32.9 1.0 CG B:HIS177 4.6 24.8 1.0 ND1 B:HIS177 4.6 28.9 1.0 O B:HOH2189 4.7 26.8 1.0 CB B:ASN174 4.7 32.0 1.0

M.Vedadi, J.Lew, J.Artz, M.Amani, Y.Zhao, A.Dong, G.A.Wasney, M.Gao, T.Hills, S.Brokx, W.Qiu, S.Sharma, A.Diassiti, Z.Alam, M.Melone, A.Mulichak, A.Wernimont, J.Bray, P.Loppnau, O.Plotnikova, K.Newberry, E.Sundararajan, S.Houston, J.Walker, W.Tempel, A.Bochkarev, I.Kozieradzki, A.Edwards, C.Arrowsmith, D.Roos, K.Kain, R.Hui. Genome-Scale Protein Expression and Structural Biology of Plasmodium Falciparum and Related Apicomplexan Organisms. Mol.Biochem.Parasitol. V. 151 100 2007.
ISSN: ISSN 0166-6851
PubMed: 17125854
DOI: 10.1016/J.MOLBIOPARA.2006.10.011