Manganese in PDB 6k5l: The Crystal Structure of Isocitrate Dehydrogenase Kinase/Phosphatase Wtih Two MN2+ From E. Coli

The structure of The Crystal Structure of Isocitrate Dehydrogenase Kinase/Phosphatase Wtih Two MN2+ From E. Coli, PDB code: 6k5l was solved by X.Zhang, Z.Lei, J.Zheng, Z.Jia, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.48 / 2.55
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	124.484, 124.484, 266.824, 90.00, 90.00, 90.00
R / Rfree (%)	19.2 / 22.1

The binding sites of Manganese atom in the The Crystal Structure of Isocitrate Dehydrogenase Kinase/Phosphatase Wtih Two MN2+ From E. Coli (pdb code 6k5l). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 4 binding sites of Manganese where determined in the The Crystal Structure of Isocitrate Dehydrogenase Kinase/Phosphatase Wtih Two MN2+ From E. Coli, PDB code: 6k5l:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in the The Crystal Structure of Isocitrate Dehydrogenase Kinase/Phosphatase Wtih Two MN2+ From E. Coli


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of The Crystal Structure of Isocitrate Dehydrogenase Kinase/Phosphatase Wtih Two MN2+ From E. Coli within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn1003 b:34.4 occ:1.00 ND2 A:ASN462 2.0 31.2 1.0 OD2 A:ASP475 2.1 39.8 1.0 O2A A:ADP1002 2.1 26.9 1.0 O2B A:ADP1002 2.1 35.0 1.0 HD21 A:ASN462 2.2 37.5 1.0 CG A:ASN462 3.1 23.0 1.0 CG A:ASP475 3.1 32.9 1.0 HB2 A:ASP475 3.2 34.0 1.0 PB A:ADP1002 3.3 30.2 1.0 PA A:ADP1002 3.4 22.6 1.0 OD1 A:ASN462 3.6 22.2 1.0 H5'2 A:ADP1002 3.6 25.3 1.0 CB A:ASP475 3.7 28.2 1.0 O3A A:ADP1002 3.7 23.4 1.0 O3B A:ADP1002 3.8 31.3 1.0 HA A:ASN462 4.0 28.1 1.0 HG3 A:LYS461 4.0 33.6 1.0 MN A:MN1004 4.0 38.1 1.0 H3' A:ADP1002 4.0 29.2 1.0 OD1 A:ASP475 4.1 31.2 1.0 HB3 A:ASP475 4.2 34.0 1.0 O5' A:ADP1002 4.2 17.1 1.0 CB A:ASN462 4.3 26.3 1.0 HA2 A:GLY320 4.3 41.6 1.0 HE1 A:TYR474 4.4 29.3 1.0 C5' A:ADP1002 4.4 21.0 1.0 HD2 A:LYS461 4.4 35.1 1.0 HB3 A:ASN462 4.4 31.6 1.0 HE3 A:LYS461 4.5 46.1 1.0 O3' A:ADP1002 4.6 34.9 1.0 CA A:ASN462 4.6 23.3 1.0 O1A A:ADP1002 4.6 22.2 1.0 O1B A:ADP1002 4.6 24.0 1.0 HZ2 A:LYS461 4.8 56.4 1.0 C3' A:ADP1002 4.8 24.2 1.0 O A:LYS461 4.8 26.0 1.0 CG A:LYS461 4.9 27.9 1.0 HA A:ASP475 4.9 28.5 1.0 OD2 A:ASP457 4.9 57.6 1.0 CA A:ASP475 5.0 23.6 1.0 O A:HOH1135 5.0 54.4 1.0 CD A:LYS461 5.0 29.1 1.0 HA3 A:GLY320 5.0 41.6 1.0

Manganese binding site 2 out of 4 in the The Crystal Structure of Isocitrate Dehydrogenase Kinase/Phosphatase Wtih Two MN2+ From E. Coli


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of The Crystal Structure of Isocitrate Dehydrogenase Kinase/Phosphatase Wtih Two MN2+ From E. Coli within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn1004 b:38.1 occ:1.00 O3B A:ADP1002 2.0 31.3 1.0 OD1 A:ASP475 2.2 31.2 1.0 OD1 A:ASP477 2.3 46.0 1.0 O A:HOH1135 2.4 54.4 1.0 OD2 A:ASP475 2.5 39.8 1.0 CG A:ASP475 2.7 32.9 1.0 CG A:ASP477 2.9 44.5 1.0 OD2 A:ASP477 2.9 40.1 1.0 PB A:ADP1002 3.2 30.2 1.0 O2B A:ADP1002 3.4 35.0 1.0 HZ3 A:LYS346 3.6 90.8 1.0 HG21 A:VAL322 3.8 61.9 1.0 HG22 A:VAL322 3.8 61.9 1.0 H A:ASP477 3.9 38.4 1.0 MN A:MN1003 4.0 34.4 1.0 HG13 A:VAL322 4.1 51.7 1.0 HZ1 A:LYS346 4.1 90.8 1.0 CB A:ASP475 4.2 28.2 1.0 NZ A:LYS346 4.2 75.5 1.0 O1B A:ADP1002 4.2 24.0 1.0 HZ2 A:LYS346 4.3 90.8 1.0 CG2 A:VAL322 4.3 51.5 1.0 OE2 A:GLU478 4.3 62.7 1.0 CB A:ASP477 4.4 41.0 1.0 O3A A:ADP1002 4.4 23.4 1.0 HB3 A:ASP475 4.5 34.0 1.0 O A:HOH1112 4.6 27.8 1.0 O2A A:ADP1002 4.6 26.9 1.0 N A:ASP477 4.6 31.9 1.0 HG3 A:GLU478 4.6 62.7 1.0 HB2 A:ASP475 4.6 34.0 1.0 H A:GLU478 4.7 48.1 1.0 HB3 A:ASP477 4.7 49.3 1.0 HG11 A:VAL322 4.7 51.7 1.0 HA A:ASP475 4.7 28.5 1.0 CG1 A:VAL322 4.8 43.0 1.0 CA A:ASP475 4.9 23.6 1.0 H A:VAL322 4.9 44.5 1.0 C A:ASP475 4.9 21.5 1.0 PA A:ADP1002 4.9 22.6 1.0 HB2 A:GLU478 4.9 55.8 1.0 HB2 A:ASP477 4.9 49.3 1.0 CA A:ASP477 5.0 32.9 1.0

Manganese binding site 3 out of 4 in the The Crystal Structure of Isocitrate Dehydrogenase Kinase/Phosphatase Wtih Two MN2+ From E. Coli


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of The Crystal Structure of Isocitrate Dehydrogenase Kinase/Phosphatase Wtih Two MN2+ From E. Coli within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn1003 b:33.6 occ:1.00 O1A B:ADP1002 2.0 25.8 1.0 OD1 B:ASN462 2.0 35.5 1.0 O1B B:ADP1002 2.1 37.5 1.0 OD2 B:ASP475 2.2 43.5 1.0 CG B:ASN462 3.1 27.5 1.0 CG B:ASP475 3.3 37.6 1.0 PA B:ADP1002 3.4 26.4 1.0 HB2 B:ASP475 3.4 39.3 1.0 PB B:ADP1002 3.4 30.7 1.0 H5'1 B:ADP1002 3.5 31.1 1.0 HD21 B:ASN462 3.5 40.9 1.0 ND2 B:ASN462 3.7 34.0 1.0 O3A B:ADP1002 3.7 25.1 1.0 CB B:ASP475 3.9 32.7 1.0 HA B:ASN462 3.9 35.0 1.0 O2B B:ADP1002 4.0 26.4 1.0 H3' B:ADP1002 4.1 34.0 1.0 HG3 B:LYS461 4.1 33.4 1.0 O5' B:ADP1002 4.2 23.4 1.0 MN B:MN1004 4.2 47.6 1.0 O B:HOH1122 4.2 34.4 1.0 OD1 B:ASP475 4.3 36.4 1.0 CB B:ASN462 4.3 24.8 1.0 HE3 B:LYS461 4.3 40.4 1.0 C5' B:ADP1002 4.3 25.8 1.0 HD2 B:LYS461 4.3 31.3 1.0 HA2 B:GLY320 4.3 46.9 1.0 HZ2 B:LYS461 4.3 53.1 1.0 HE1 B:TYR474 4.3 32.5 1.0 HB3 B:ASP475 4.3 39.3 1.0 HB3 B:ASN462 4.5 29.8 1.0 CA B:ASN462 4.5 29.1 1.0 O3' B:ADP1002 4.6 36.0 1.0 HD22 B:ASN462 4.6 40.9 1.0 O3B B:ADP1002 4.6 23.3 1.0 O2A B:ADP1002 4.6 31.6 1.0 O B:LYS461 4.7 30.8 1.0 C3' B:ADP1002 4.7 28.2 1.0 CD B:LYS461 4.9 26.0 1.0 CE B:LYS461 4.9 33.5 1.0 CG B:LYS461 4.9 27.7 1.0 HA3 B:GLY320 4.9 46.9 1.0 N B:ASN462 4.9 29.6 1.0 HA B:ASP475 5.0 35.9 1.0 NZ B:LYS461 5.0 44.1 1.0

Manganese binding site 4 out of 4 in the The Crystal Structure of Isocitrate Dehydrogenase Kinase/Phosphatase Wtih Two MN2+ From E. Coli


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of The Crystal Structure of Isocitrate Dehydrogenase Kinase/Phosphatase Wtih Two MN2+ From E. Coli within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn1004 b:47.6 occ:1.00 O2B B:ADP1002 2.2 26.4 1.0 OD1 B:ASP475 2.2 36.4 1.0 OD2 B:ASP477 2.3 53.1 1.0 HZ3 B:LYS346 2.4 0.6 1.0 OD2 B:ASP475 2.6 43.5 1.0 HZ1 B:LYS346 2.6 0.6 1.0 CG B:ASP475 2.7 37.6 1.0 NZ B:LYS346 2.8 98.7 1.0 HZ2 B:LYS346 2.8 0.6 1.0 CG B:ASP477 3.0 44.2 1.0 OD1 B:ASP477 3.0 40.6 1.0 PB B:ADP1002 3.2 30.7 1.0 O1B B:ADP1002 3.4 37.5 1.0 HG21 B:VAL322 3.8 51.9 1.0 HG22 B:VAL322 3.8 51.9 1.0 HG13 B:VAL322 4.0 46.5 1.0 H B:ASP477 4.0 39.7 1.0 O3B B:ADP1002 4.2 23.3 1.0 MN B:MN1003 4.2 33.6 1.0 CB B:ASP475 4.2 32.7 1.0 CE B:LYS346 4.3 0.0 1.0 CG2 B:VAL322 4.3 43.1 1.0 HB2 B:GLU478 4.4 59.4 1.0 CB B:ASP477 4.4 39.5 1.0 O3A B:ADP1002 4.5 25.1 1.0 HE2 B:LYS346 4.5 0.1 1.0 HG11 B:VAL322 4.5 46.5 1.0 H B:GLU478 4.6 44.2 1.0 HB3 B:ASP475 4.6 39.3 1.0 O1A B:ADP1002 4.6 25.8 1.0 CG1 B:VAL322 4.6 38.6 1.0 HB2 B:ASP475 4.7 39.3 1.0 HD3 B:LYS346 4.7 0.9 1.0 N B:ASP477 4.7 33.0 1.0 HB3 B:ASP477 4.7 47.6 1.0 HA B:ASP475 4.7 35.9 1.0 HE3 B:LYS346 4.8 0.1 1.0 OE1 B:GLU478 4.9 61.4 1.0 CA B:ASP475 4.9 29.8 1.0 H B:VAL322 4.9 42.9 1.0 N B:GLU478 4.9 36.7 1.0 CA B:ASP477 5.0 35.1 1.0

X.Zhang, Z.Lei, J.Zhang, Z.Jia. The Crystal Structure of Isocitrate Dehydrogenase Kinase/Phosphatase Wtih Two MN2+ From E. Coli To Be Published.