Cobalt in PDB 2gve: Time-of-Flight Neutron Diffraction Structure of D-Xylose Isomerase

All present enzymatic activity of Time-of-Flight Neutron Diffraction Structure of D-Xylose Isomerase:
5.3.1.5;

The binding sites of Cobalt atom in the Time-of-Flight Neutron Diffraction Structure of D-Xylose Isomerase (pdb code 2gve). This binding sites where shown within 5.0 Angstroms radius around Cobalt atom.
In total 2 binding sites of Cobalt where determined in the Time-of-Flight Neutron Diffraction Structure of D-Xylose Isomerase, PDB code: 2gve:
Jump to Cobalt binding site number: 1; 2;

Cobalt binding site 1 out of 2 in the Time-of-Flight Neutron Diffraction Structure of D-Xylose Isomerase


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 1 of Time-of-Flight Neutron Diffraction Structure of D-Xylose Isomerase within 5.0Å range: probe atom residue distance (Å) B Occ A:Co390 b:11.6 occ:1.00 OD2 A:ASP255 1.9 8.6 1.0 O A:DOD1018 2.0 10.0 1.0 DE2 A:HIS220 2.0 9.5 0.4 D1 A:DOD1018 2.0 15.0 1.0 OE2 A:GLU217 2.1 5.9 1.0 OD1 A:ASP257 2.2 6.6 1.0 D2 A:DOD1018 2.3 15.0 1.0 CG A:ASP255 2.6 9.1 1.0 OD1 A:ASP255 2.6 6.8 1.0 NE2 A:HIS220 2.7 7.9 1.0 D1 A:DOD1174 2.8 38.2 1.0 HD2 A:HIS220 2.9 7.6 1.0 D1 A:DOD3452 3.0 59.8 1.0 CD A:GLU217 3.0 8.5 1.0 CD2 A:HIS220 3.1 6.3 1.0 CG A:ASP257 3.1 10.8 1.0 OD2 A:ASP257 3.3 12.1 1.0 OE1 A:GLU217 3.3 7.1 1.0 D2 A:DOD1021 3.4 10.9 1.0 O A:DOD1174 3.6 25.4 1.0 DD22 A:ASN247 3.6 10.1 1.0 O A:DOD3452 3.7 39.9 1.0 HD21 A:ASN247 3.8 10.1 0.0 DD21 A:ASN247 3.8 10.1 1.0 CE1 A:HIS220 3.9 9.6 1.0 CB A:ASP255 4.1 6.2 1.0 ND2 A:ASN247 4.1 8.4 1.0 HE3 A:LYS183 4.2 16.1 1.0 O A:DOD1021 4.2 7.3 1.0 HE1 A:HIS220 4.3 11.5 1.0 DZ3 A:LYS183 4.3 19.5 1.0 D2 A:DOD3452 4.3 59.8 1.0 HB3 A:ASP255 4.3 7.4 1.0 D2 A:DOD1174 4.3 38.2 1.0 CG A:HIS220 4.4 8.1 1.0 CG A:GLU217 4.4 5.5 1.0 HA A:ASP257 4.4 11.0 1.0 CB A:ASP257 4.5 5.2 1.0 HB2 A:ASP255 4.5 7.4 1.0 HG2 A:GLU217 4.5 6.6 1.0 ND1 A:HIS220 4.7 7.9 1.0 DZ1 A:LYS183 4.7 19.5 1.0 D1 A:DOD1116 4.8 52.0 1.0 CO A:CO391 4.8 16.8 1.0 NZ A:LYS183 4.8 16.3 1.0 OD2 A:ASP287 4.8 17.7 1.0 HA3 A:GLY219 4.9 9.7 1.0 H A:HIS220 4.9 11.2 0.9 D A:HIS220 4.9 11.2 0.1 HB2 A:ASP257 4.9 6.3 1.0 CA A:ASP257 4.9 9.2 1.0 H A:ASP257 4.9 12.3 0.2 D A:ASP257 4.9 12.3 0.8 HA A:ASP255 4.9 8.1 1.0 D1 A:DOD1021 4.9 10.9 1.0 CE A:LYS183 5.0 13.4 1.0 HB3 A:GLU217 5.0 5.3 1.0

Cobalt binding site 2 out of 2 in the Time-of-Flight Neutron Diffraction Structure of D-Xylose Isomerase


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 2 of Time-of-Flight Neutron Diffraction Structure of D-Xylose Isomerase within 5.0Å range: probe atom residue distance (Å) B Occ A:Co391 b:16.8 occ:1.00 OE1 A:GLU217 2.0 7.1 1.0 OE2 A:GLU181 2.0 15.0 1.0 OD2 A:ASP287 2.1 17.7 1.0 D1 A:DOD1116 2.2 52.0 1.0 D2 A:DOD1218 2.2 13.2 1.0 O A:DOD1218 2.2 8.8 1.0 O A:DOD1116 2.5 34.6 1.0 OD2 A:ASP245 2.5 9.7 1.0 D1 A:DOD1218 2.5 13.2 1.0 CD A:GLU181 2.9 15.1 1.0 D1 A:DOD1018 3.0 15.0 1.0 CG A:ASP287 3.1 18.4 1.0 OE1 A:GLU181 3.2 16.5 1.0 CD A:GLU217 3.2 8.5 1.0 D2 A:DOD1116 3.3 52.0 1.0 HB3 A:ASP287 3.4 15.4 1.0 D1 A:DOD1240 3.5 50.3 1.0 CG A:ASP245 3.5 11.2 1.0 HB2 A:ASP287 3.6 15.4 1.0 HB2 A:GLU217 3.6 5.3 1.0 HE1 A:HIS220 3.6 11.5 1.0 O A:DOD1018 3.6 10.0 1.0 CB A:ASP287 3.6 12.9 1.0 HB3 A:ASP245 3.6 8.7 1.0 D2 A:DOD1240 3.7 50.3 1.0 HG3 A:GLU217 3.8 6.6 1.0 HB2 A:ASP245 3.8 8.7 1.0 CB A:ASP245 3.9 7.2 1.0 CG A:GLU217 3.9 5.5 1.0 CE1 A:HIS220 4.0 9.6 1.0 O A:DOD1240 4.0 33.5 1.0 OE2 A:GLU217 4.1 5.9 1.0 HD21 A:ASN215 4.2 24.1 0.1 DD21 A:ASN215 4.2 24.1 0.9 D2 A:DOD1018 4.2 15.0 1.0 CB A:GLU217 4.2 4.4 1.0 OD1 A:ASP287 4.2 14.1 1.0 CG A:GLU181 4.3 10.2 1.0 DE2 A:HIS220 4.3 9.5 0.4 NE2 A:HIS220 4.4 7.9 1.0 HG2 A:GLU181 4.5 12.2 1.0 D1 A:DOD1022 4.5 5.8 0.5 HG3 A:GLU181 4.5 12.2 1.0 HB3 A:GLU217 4.7 5.3 1.0 D1 A:DOD1174 4.7 38.2 1.0 HZ2 A:TRP16 4.7 16.8 1.0 OD1 A:ASP245 4.7 10.3 1.0 ND1 A:HIS220 4.8 7.9 1.0 CO A:CO390 4.8 11.6 1.0 ND2 A:ASN215 4.8 20.1 1.0 HG2 A:GLU217 4.8 6.6 1.0 HD22 A:ASN215 5.0 24.1 0.2 DD22 A:ASN215 5.0 24.1 0.8

A.K.Katz, X.Li, H.L.Carrell, B.L.Hanson, P.Langan, L.Coates, B.P.Schoenborn, J.P.Glusker, G.J.Bunick. Locating Active-Site Hydrogen Atoms in D-Xylose Isomerase: Time-of-Flight Neutron Diffraction. Proc.Natl.Acad.Sci.Usa V. 103 8342 2006.
ISSN: ISSN 0027-8424
PubMed: 16707576
DOI: 10.1073/PNAS.0602598103