Manganese in PDB 6lna: Ydiu Complex with Ampnpp and MN2+

The structure of Ydiu Complex with Ampnpp and MN2+, PDB code: 6lna was solved by B.Li, Y.Yang, Y.Ma, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	27.44 / 1.70
Space group	I 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	112.43, 73.541, 122.649, 90, 102.49, 90
R / Rfree (%)	14 / 18.6

The structure of Ydiu Complex with Ampnpp and MN2+ also contains other interesting chemical elements:

Calcium

(Ca)

2 atoms

The binding sites of Manganese atom in the Ydiu Complex with Ampnpp and MN2+ (pdb code 6lna). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 4 binding sites of Manganese where determined in the Ydiu Complex with Ampnpp and MN2+, PDB code: 6lna:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in the Ydiu Complex with Ampnpp and MN2+


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Ydiu Complex with Ampnpp and MN2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn501 b:4.6 occ:1.00 ND2 A:ASN247 2.1 2.1 1.0 O1G A:ANP503 2.1 5.0 1.0 OD2 A:ASP256 2.2 4.3 1.0 O A:HOH658 2.2 3.8 1.0 O1A A:ANP503 2.3 4.6 1.0 O3A A:ANP503 2.5 5.8 1.0 PA A:ANP503 2.9 4.8 1.0 CG A:ASN247 3.1 3.7 1.0 CG A:ASP256 3.2 6.2 1.0 PG A:ANP503 3.4 3.8 1.0 OD1 A:ASN247 3.5 7.1 1.0 PB A:ANP503 3.6 5.0 1.0 CB A:ASP256 3.6 4.2 1.0 N3B A:ANP503 3.6 2.1 1.0 O2A A:ANP503 3.8 4.5 1.0 OD2 A:ASP246 4.0 5.5 1.0 NH1 A:ARG177 4.0 2.8 1.0 O3G A:ANP503 4.1 3.6 1.0 O2B A:ANP503 4.1 3.0 1.0 O5' A:ANP503 4.2 6.6 1.0 OD1 A:ASP256 4.2 4.1 1.0 MN A:MN502 4.3 8.5 1.0 CB A:ASN247 4.4 3.3 1.0 OH A:TYR71 4.4 5.2 1.0 O A:HOH659 4.5 5.3 1.0 O2G A:ANP503 4.6 4.7 1.0 C5' A:ANP503 4.6 4.8 1.0 O A:ASP246 4.7 3.6 1.0 CA A:ASN247 4.8 3.3 1.0 O1B A:ANP503 4.9 6.2 1.0 C3' A:ANP503 5.0 4.0 1.0 CG A:ASP246 5.0 3.1 1.0

Manganese binding site 2 out of 4 in the Ydiu Complex with Ampnpp and MN2+


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Ydiu Complex with Ampnpp and MN2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn502 b:8.5 occ:1.00 O2B A:ANP503 2.3 3.0 1.0 O2A A:ANP503 2.3 4.5 1.0 OD1 A:ASP256 2.4 4.1 1.0 O A:HOH1146 2.4 6.5 1.0 O A:HOH1075 2.5 6.9 1.0 O A:HOH991 2.5 5.0 1.0 OD2 A:ASP256 2.6 4.3 1.0 CG A:ASP256 2.9 6.2 1.0 PA A:ANP503 3.4 4.8 1.0 PB A:ANP503 3.5 5.0 1.0 O3A A:ANP503 3.6 5.8 1.0 NH1 A:ARG87 3.9 6.0 1.0 O1A A:ANP503 4.1 4.6 1.0 NZ A:LYS107 4.1 4.9 1.0 O A:HOH620 4.2 8.1 1.0 O A:HOH704 4.3 16.9 1.0 MN A:MN501 4.3 4.6 1.0 CB A:ASP256 4.4 4.2 1.0 O A:ASP256 4.5 3.2 1.0 N3B A:ANP503 4.5 2.1 1.0 O A:HOH1310 4.5 12.9 1.0 O A:HOH1246 4.5 13.5 1.0 O1B A:ANP503 4.6 6.2 1.0 O3G A:ANP503 4.7 3.6 1.0 O5' A:ANP503 4.7 6.6 1.0 CA A:GLY258 4.7 5.3 1.0 O A:HOH1178 4.7 23.1 1.0 O A:HOH1399 4.8 20.2 1.0 O A:TYR257 4.8 5.2 1.0 C A:ASP256 4.9 3.2 1.0 CE A:LYS107 4.9 4.7 1.0 N A:GLY258 4.9 4.3 1.0 C A:TYR257 5.0 3.0 1.0

Manganese binding site 3 out of 4 in the Ydiu Complex with Ampnpp and MN2+


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Ydiu Complex with Ampnpp and MN2+ within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn501 b:5.3 occ:1.00 O1G B:ANP503 2.1 6.9 1.0 OD1 B:ASN247 2.1 4.5 1.0 O B:HOH710 2.1 5.3 1.0 OD2 B:ASP256 2.2 5.8 1.0 O2A B:ANP503 2.3 5.7 1.0 O3A B:ANP503 2.4 9.0 1.0 PA B:ANP503 2.9 7.0 1.0 CG B:ASN247 3.1 6.7 1.0 CG B:ASP256 3.2 6.0 1.0 PG B:ANP503 3.3 4.6 1.0 ND2 B:ASN247 3.5 4.8 1.0 PB B:ANP503 3.5 5.7 1.0 CB B:ASP256 3.6 3.5 1.0 N3B B:ANP503 3.6 2.9 1.0 O1A B:ANP503 3.8 5.1 1.0 NH1 B:ARG177 4.0 3.1 1.0 OD2 B:ASP246 4.0 7.5 1.0 O1B B:ANP503 4.1 6.3 1.0 O3G B:ANP503 4.1 5.6 1.0 O5' B:ANP503 4.1 7.5 1.0 OD1 B:ASP256 4.2 5.3 1.0 MN B:MN502 4.3 9.6 1.0 OH B:TYR71 4.5 5.4 1.0 CB B:ASN247 4.5 6.5 1.0 O2G B:ANP503 4.5 5.5 1.0 O B:HOH796 4.6 6.5 1.0 C5' B:ANP503 4.6 5.2 1.0 O B:ASP246 4.7 4.7 1.0 CA B:ASN247 4.8 3.8 1.0 O2B B:ANP503 4.8 7.0 1.0 C3' B:ANP503 4.9 4.6 1.0 CG B:ASP246 5.0 4.8 1.0

Manganese binding site 4 out of 4 in the Ydiu Complex with Ampnpp and MN2+


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Ydiu Complex with Ampnpp and MN2+ within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn502 b:9.6 occ:1.00 O1B B:ANP503 2.3 6.3 1.0 OD1 B:ASP256 2.3 5.3 1.0 O B:HOH1146 2.4 7.2 1.0 O1A B:ANP503 2.4 5.1 1.0 O B:HOH1074 2.4 9.0 1.0 O B:HOH960 2.5 7.5 1.0 OD2 B:ASP256 2.6 5.8 1.0 CG B:ASP256 2.8 6.0 1.0 PA B:ANP503 3.4 7.0 1.0 PB B:ANP503 3.5 5.7 1.0 O3A B:ANP503 3.6 9.0 1.0 NH1 B:ARG87 3.9 7.9 1.0 NZ B:LYS107 4.1 7.8 1.0 O2A B:ANP503 4.1 5.7 1.0 O B:HOH620 4.1 7.6 1.0 MN B:MN501 4.3 5.3 1.0 O B:HOH907 4.3 23.4 1.0 CB B:ASP256 4.4 3.5 1.0 O B:HOH784 4.5 11.2 1.0 O B:HOH1318 4.5 12.6 1.0 N3B B:ANP503 4.5 2.9 1.0 O B:HOH1061 4.5 22.6 1.0 O2B B:ANP503 4.5 7.0 1.0 O B:ASP256 4.6 4.7 1.0 O3G B:ANP503 4.7 5.6 1.0 O5' B:ANP503 4.7 7.5 1.0 O B:HOH1414 4.8 16.6 1.0 CA B:GLY258 4.8 5.8 1.0 O B:TYR257 4.8 7.8 1.0 C B:ASP256 4.9 6.8 1.0 CE B:LYS107 4.9 7.4 1.0 N B:GLY258 5.0 5.9 1.0

B.Li, B.Li, Y.Yang, Y.Ma. N/A N/A.