Cobalt in PDB 2ywr: Crystal Structure of Gar Transformylase From Aquifex Aeolicus

All present enzymatic activity of Crystal Structure of Gar Transformylase From Aquifex Aeolicus:
2.1.2.2;

The structure of Crystal Structure of Gar Transformylase From Aquifex Aeolicus, PDB code: 2ywr was solved by M.Kanagawa, S.Baba, S.Kuramitsu, S.Yokoyama, G.Kawai, G.Sampei, Rikenstructural Genomics/Proteomics Initiative (Rsgi), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	42.40 / 1.77
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	59.955, 59.955, 105.934, 90.00, 90.00, 90.00
R / Rfree (%)	20.4 / 21.9

The structure of Crystal Structure of Gar Transformylase From Aquifex Aeolicus also contains other interesting chemical elements:

Magnesium

(Mg)

1 atom

The binding sites of Cobalt atom in the Crystal Structure of Gar Transformylase From Aquifex Aeolicus (pdb code 2ywr). This binding sites where shown within 5.0 Angstroms radius around Cobalt atom.
In total 4 binding sites of Cobalt where determined in the Crystal Structure of Gar Transformylase From Aquifex Aeolicus, PDB code: 2ywr:
Jump to Cobalt binding site number: 1; 2; 3; 4;

Cobalt binding site 1 out of 4 in the Crystal Structure of Gar Transformylase From Aquifex Aeolicus


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 Gar Transformylase From Aquifex Aeolicus within 5.0Å range: probe atom residue distance (Å) B Occ A:Co704 b:29.3 occ:1.00 O A:HOH774 2.2 20.4 1.0 ND1 A:HIS109 2.3 12.3 1.0 CE1 A:HIS109 3.1 14.8 1.0 O A:HOH905 3.1 51.4 1.0 CG A:HIS109 3.4 14.6 1.0 OD1 A:ASP145 3.4 35.3 1.0 CB A:HIS109 3.8 13.9 1.0 ND2 A:ASN107 3.9 20.2 1.0 CG A:ASP145 4.0 34.6 1.0 OD2 A:ASP145 4.2 35.1 1.0 CA A:HIS109 4.2 14.1 1.0 NE2 A:HIS109 4.3 11.4 1.0 O A:HOH1007 4.4 40.9 1.0 CD2 A:HIS109 4.4 14.4 1.0 O A:GLY118 4.4 20.0 1.0 O A:HOH901 4.5 27.2 1.0 CD A:PRO110 4.6 12.9 1.0 O A:ILE108 4.6 13.8 1.0 CG A:ASN107 5.0 18.9 1.0

Cobalt binding site 2 out of 4 in the Crystal Structure of Gar Transformylase From Aquifex Aeolicus


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 Gar Transformylase From Aquifex Aeolicus within 5.0Å range: probe atom residue distance (Å) B Occ A:Co727 b:67.6 occ:1.00 O A:VAL157 2.8 17.1 1.0 O A:HOH768 2.9 14.5 1.0 O A:HOH929 3.0 35.9 1.0 N A:PRO159 3.3 19.7 1.0 C A:LEU158 3.3 18.9 1.0 NZ A:LYS131 3.4 23.8 1.0 C A:VAL157 3.4 16.9 1.0 CD A:PRO159 3.6 19.3 1.0 CD A:LYS131 3.6 19.5 1.0 O A:LEU158 3.7 19.8 1.0 CA A:LEU158 3.7 19.2 1.0 CA A:PRO159 3.8 20.0 1.0 N A:LEU158 3.9 17.2 1.0 CG A:PRO159 3.9 20.9 1.0 CE A:LYS131 4.1 19.6 1.0 CG1 A:VAL157 4.2 17.4 1.0 CB A:VAL157 4.3 15.7 1.0 O A:VAL130 4.4 15.5 1.0 O A:HOH919 4.4 39.0 1.0 CA A:VAL157 4.5 15.9 1.0 CB A:PRO159 4.5 20.1 1.0 CA A:LYS131 4.8 13.3 1.0 O A:HOH779 4.8 18.5 1.0

Cobalt binding site 3 out of 4 in the Crystal Structure of Gar Transformylase From Aquifex Aeolicus


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 Gar Transformylase From Aquifex Aeolicus within 5.0Å range: probe atom residue distance (Å) B Occ A:Co766 b:30.7 occ:1.00 O A:HOH1004 2.1 28.3 1.0 O A:HOH1010 2.2 31.0 1.0 NZ A:LYS79 2.3 29.9 1.0 O A:HOH909 2.3 27.0 1.0 O A:HOH973 2.4 31.1 1.0 CE A:LYS79 3.2 26.4 1.0 OE1 A:GLU53 3.4 28.0 1.0 O A:HOH959 3.7 45.2 1.0 OE1 A:GLU32 4.1 19.7 1.0 O A:GLU32 4.2 14.4 1.0 CD A:GLU53 4.5 27.4 1.0 CD A:LYS79 4.6 26.2 1.0 O A:HOH787 4.7 22.2 1.0 CB A:GLU53 4.8 20.2 1.0

Cobalt binding site 4 out of 4 in the Crystal Structure of Gar Transformylase From Aquifex Aeolicus


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 Gar Transformylase From Aquifex Aeolicus within 5.0Å range: probe atom residue distance (Å) B Occ A:Co767 b:0.8 occ:1.00 O A:HOH822 2.8 22.3 1.0 CB A:CYS54 2.9 21.9 1.0 O A:ILE44 3.1 16.9 1.0 NZ A:LYS48 3.3 34.3 1.0 CG2 A:ILE44 3.4 18.5 1.0 CG A:LYS48 3.5 27.7 1.0 CB A:CYS47 3.5 16.8 1.0 SG A:CYS54 3.7 26.7 1.0 O A:HOH831 3.8 40.8 1.0 O A:HOH958 3.9 45.7 1.0 C A:ILE44 4.0 18.1 1.0 CE A:LYS48 4.0 33.0 1.0 N A:LYS48 4.0 19.7 1.0 CA A:ILE44 4.2 17.5 1.0 CA A:CYS54 4.2 20.8 1.0 CB A:ILE44 4.4 19.6 1.0 CD A:LYS48 4.4 30.3 1.0 C A:CYS47 4.4 17.8 1.0 N A:CYS54 4.4 17.9 1.0 CA A:CYS47 4.5 16.1 1.0 O A:VAL52 4.5 15.4 1.0 CA A:LYS48 4.6 20.1 1.0 CB A:LYS48 4.7 23.4 1.0 O A:CYS54 4.7 21.2 1.0 SG A:CYS47 4.7 17.1 1.0 C A:CYS54 4.7 21.1 1.0 O A:HOH885 4.7 21.9 1.0 O A:HOH976 5.0 43.7 1.0

G.Sampei, M.Kanagawa, S.Baba, T.Shimasaki, H.Taka, S.Mitsui, S.Fujiwara, Y.Yanagida, M.Kusano, S.Suzuki, K.Terao, H.Kawai, Y.Fukai, N.Nakagawa, A.Ebihara, S.Kuramitsu, S.Yokoyama, G.Kawai. Structures and Reaction Mechanisms of the Two Related Enzymes, Purn and Puru. J.Biochem. V. 154 569 2013.
ISSN: ISSN 0021-924X
PubMed: 24108189
DOI: 10.1093/JB/MVT090