Manganese in PDB 1gq2: Malic Enzyme From Pigeon Liver

All present enzymatic activity of Malic Enzyme From Pigeon Liver:
1.1.1.40;

The structure of Malic Enzyme From Pigeon Liver, PDB code: 1gq2 was solved by Z.Yang, H.Zhang, T.Liang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	10 / 2.5
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	124.149, 140.863, 167.079, 90.05, 87.16, 75.63
R / Rfree (%)	21 / 25.6

The structure of Malic Enzyme From Pigeon Liver also contains other interesting chemical elements:

Chlorine	(Cl)	33 atoms
Sodium	(Na)	36 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 16;

Binding sites:

The binding sites of Manganese atom in the Malic Enzyme From Pigeon Liver (pdb code 1gq2). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 16 binding sites of Manganese where determined in the Malic Enzyme From Pigeon Liver, PDB code: 1gq2:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Manganese binding site 1 out of 16 in the Malic Enzyme From Pigeon Liver


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Malic Enzyme From Pigeon Liver within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn1584 b:15.3 occ:1.00 OD1 A:ASP279 2.3 9.4 1.0 O2 A:OXL1583 2.3 42.2 1.0 OE2 A:GLU255 2.4 22.1 1.0 OD1 A:ASP256 2.4 17.4 1.0 O3 A:OXL1583 2.5 41.7 1.0 C2 A:OXL1583 2.9 42.2 1.0 C1 A:OXL1583 3.0 42.3 1.0 CG A:ASP256 3.0 15.2 1.0 OD2 A:ASP256 3.2 14.8 1.0 CD A:GLU255 3.3 20.4 1.0 CG A:ASP279 3.5 14.7 1.0 NZ A:LYS183 3.6 18.5 1.0 CG A:GLU255 3.7 16.7 1.0 OD2 A:ASP279 4.1 15.8 1.0 O1 A:OXL1583 4.1 43.2 1.0 O4 A:OXL1583 4.1 41.1 1.0 CE A:LYS183 4.1 18.1 1.0 N A:ASP256 4.2 13.8 1.0 NH2 A:ARG165 4.2 16.3 1.0 NH1 A:ARG165 4.3 15.6 1.0 CB A:ASP256 4.3 14.2 1.0 OE1 A:GLU255 4.4 21.5 1.0 ND2 A:ASN467 4.4 29.4 1.0 CA A:ASP256 4.6 13.8 1.0 CZ A:ARG165 4.6 14.9 1.0 CB A:ASP279 4.7 14.9 1.0 CB A:GLU255 4.9 13.9 1.0 C5N A:NAP1581 4.9 32.6 1.0

Manganese binding site 2 out of 16 in the Malic Enzyme From Pigeon Liver


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Malic Enzyme From Pigeon Liver within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn1583 b:15.6 occ:1.00 OD1 B:ASP279 2.3 14.0 1.0 OE2 B:GLU255 2.3 17.5 1.0 OD2 B:ASP256 2.3 11.3 1.0 O3 B:OXL1582 2.3 46.9 1.0 O2 B:OXL1582 2.4 50.4 1.0 C1 B:OXL1582 2.9 48.4 1.0 C2 B:OXL1582 3.0 49.0 1.0 CD B:GLU255 3.2 15.6 1.0 CG B:ASP279 3.2 16.4 1.0 CG B:ASP256 3.3 14.0 1.0 OD2 B:ASP279 3.4 16.9 1.0 NZ B:LYS183 3.6 14.3 1.0 NH2 B:ARG165 3.6 20.8 1.0 OD1 B:ASP256 3.6 15.9 1.0 CG B:GLU255 3.7 15.7 1.0 CE B:LYS183 3.8 12.1 1.0 ND2 B:ASN467 4.0 21.3 1.0 O1 B:OXL1582 4.1 47.9 1.0 OE1 B:GLU255 4.1 17.0 1.0 O4 B:OXL1582 4.2 49.8 1.0 N B:ASP256 4.4 13.4 1.0 C5N B:NAP1581 4.6 31.1 1.0 CB B:ASP279 4.6 15.4 1.0 CB B:ASP256 4.6 12.8 1.0 CZ B:ARG165 4.7 19.3 1.0 O B:HOH2042 4.7 13.2 1.0 CA B:ASP256 4.8 13.7 1.0 CD2 B:LEU167 4.9 7.3 1.0 OD2 B:ASP278 5.0 18.2 1.0 C4N B:NAP1581 5.0 31.2 1.0 CA B:ASP279 5.0 14.2 1.0

Manganese binding site 3 out of 16 in the Malic Enzyme From Pigeon Liver


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Malic Enzyme From Pigeon Liver within 5.0Å range: probe atom residue distance (Å) B Occ C:Mn1583 b:9.3 occ:1.00 OD1 C:ASP279 2.2 13.1 1.0 O2 C:OXL1582 2.2 24.9 1.0 OD1 C:ASP256 2.3 15.3 1.0 OE1 C:GLU255 2.3 7.6 1.0 O3 C:OXL1582 2.4 28.4 1.0 O C:HOH2077 2.4 3.3 1.0 C2 C:OXL1582 3.0 28.5 1.0 C1 C:OXL1582 3.0 28.8 1.0 CG C:ASP279 3.1 14.4 1.0 CD C:GLU255 3.3 8.9 1.0 OD2 C:ASP279 3.3 16.2 1.0 CG C:ASP256 3.4 14.1 1.0 CG C:GLU255 3.7 8.7 1.0 OD2 C:ASP256 3.9 12.9 1.0 NZ C:LYS183 3.9 14.7 1.0 CE C:LYS183 4.2 15.0 1.0 N C:ASP256 4.2 12.3 1.0 O4 C:OXL1582 4.2 30.7 1.0 O1 C:OXL1582 4.2 27.0 1.0 NH2 C:ARG165 4.3 10.4 1.0 ND2 C:ASN467 4.3 20.1 1.0 NH1 C:ARG165 4.4 11.1 1.0 CB C:ASP279 4.4 12.5 1.0 OE2 C:GLU255 4.4 10.1 1.0 C5N C:NAP1581 4.4 11.6 1.0 CB C:ASP256 4.6 12.9 1.0 CA C:ASP256 4.7 12.8 1.0 C4N C:NAP1581 4.8 10.2 1.0 CZ C:ARG165 4.8 9.9 1.0 CA C:ASP279 4.8 12.1 1.0 OD2 C:ASP278 4.9 17.7 1.0 O C:HOH2004 4.9 10.7 1.0 N C:ASP279 5.0 11.6 1.0 CB C:GLU255 5.0 10.0 1.0

Manganese binding site 4 out of 16 in the Malic Enzyme From Pigeon Liver


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Malic Enzyme From Pigeon Liver within 5.0Å range: probe atom residue distance (Å) B Occ D:Mn1583 b:17.9 occ:1.00 O2 D:OXL1582 2.1 20.0 1.0 OD1 D:ASP256 2.1 12.1 1.0 OE2 D:GLU255 2.2 5.2 1.0 OD1 D:ASP279 2.2 21.5 1.0 O3 D:OXL1582 2.4 12.3 1.0 O D:HOH2049 2.5 12.1 1.0 C2 D:OXL1582 2.9 18.7 1.0 C1 D:OXL1582 3.0 16.2 1.0 CG D:ASP256 3.2 15.0 1.0 CD D:GLU255 3.3 6.8 1.0 CG D:ASP279 3.4 20.8 1.0 OD2 D:ASP256 3.7 15.8 1.0 CG D:GLU255 3.8 5.3 1.0 OD2 D:ASP279 4.0 22.8 1.0 NZ D:LYS183 4.1 8.0 1.0 NH2 D:ARG165 4.1 19.1 1.0 N D:ASP256 4.1 12.3 1.0 O4 D:OXL1582 4.1 22.1 1.0 NH1 D:ARG165 4.2 20.5 1.0 O1 D:OXL1582 4.2 15.7 1.0 C5N D:NAP1581 4.4 14.5 1.0 ND2 D:ASN467 4.4 18.9 1.0 CE D:LYS183 4.4 7.2 1.0 OE1 D:GLU255 4.4 11.2 1.0 CB D:ASP256 4.5 13.3 1.0 CZ D:ARG165 4.6 19.9 1.0 CB D:ASP279 4.6 17.4 1.0 CA D:ASP256 4.6 13.1 1.0 OD2 D:ASP278 4.8 21.1 1.0 C6N D:NAP1581 4.9 13.7 1.0 C4N D:NAP1581 4.9 13.5 1.0 CA D:ASP279 4.9 15.2 1.0 CD2 D:LEU167 4.9 8.7 1.0 C D:GLU255 5.0 11.2 1.0

Manganese binding site 5 out of 16 in the Malic Enzyme From Pigeon Liver


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 5 of Malic Enzyme From Pigeon Liver within 5.0Å range: probe atom residue distance (Å) B Occ E:Mn1583 b:17.1 occ:1.00 OD1 E:ASP279 2.1 17.5 1.0 O2 E:OXL1582 2.2 20.9 1.0 O3 E:OXL1582 2.2 18.8 1.0 OD2 E:ASP256 2.2 10.9 1.0 OE1 E:GLU255 2.4 15.8 1.0 O E:HOH2058 2.4 4.1 1.0 C2 E:OXL1582 2.8 22.9 1.0 C1 E:OXL1582 2.9 22.2 1.0 CG E:ASP256 3.3 10.5 1.0 CD E:GLU255 3.3 15.5 1.0 CG E:ASP279 3.4 18.6 1.0 OD1 E:ASP256 3.7 11.5 1.0 NH2 E:ARG165 3.8 12.7 1.0 CG E:GLU255 3.8 13.6 1.0 O1 E:OXL1582 4.0 22.3 1.0 NH1 E:ARG165 4.0 10.2 1.0 O4 E:OXL1582 4.1 23.9 1.0 OD2 E:ASP279 4.1 20.6 1.0 N E:ASP256 4.2 11.9 1.0 ND2 E:ASN467 4.2 24.1 1.0 CZ E:ARG165 4.4 10.9 1.0 CB E:ASP279 4.4 16.3 1.0 NZ E:LYS183 4.4 16.1 1.0 OE2 E:GLU255 4.4 16.6 1.0 C5N E:NAP1581 4.5 29.0 1.0 CB E:ASP256 4.6 9.9 1.0 CE E:LYS183 4.6 14.9 1.0 CA E:ASP279 4.6 15.4 1.0 CA E:ASP256 4.6 12.0 1.0 N E:ASP279 4.8 15.9 1.0 C4N E:NAP1581 4.9 28.7 1.0 C6N E:NAP1581 5.0 28.5 1.0 OD2 E:ASP278 5.0 17.5 1.0

Manganese binding site 6 out of 16 in the Malic Enzyme From Pigeon Liver


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 6 of Malic Enzyme From Pigeon Liver within 5.0Å range: probe atom residue distance (Å) B Occ F:Mn1583 b:13.9 occ:1.00 O3 F:OXL1582 2.2 19.4 1.0 OD1 F:ASP279 2.2 13.3 1.0 O2 F:OXL1582 2.3 20.2 1.0 OD1 F:ASP256 2.4 10.6 1.0 O F:HOH2078 2.4 4.8 1.0 OE2 F:GLU255 2.4 18.2 1.0 C1 F:OXL1582 2.9 21.5 1.0 C2 F:OXL1582 2.9 21.8 1.0 CG F:ASP279 3.2 15.2 1.0 CG F:ASP256 3.3 11.6 1.0 OD2 F:ASP279 3.4 16.7 1.0 CD F:GLU255 3.4 18.0 1.0 OE1 F:GLU255 3.7 21.3 1.0 OD2 F:ASP256 3.8 10.1 1.0 NZ F:LYS183 4.0 8.7 1.0 O1 F:OXL1582 4.1 19.0 1.0 NH1 F:ARG165 4.2 14.2 1.0 N F:ASP256 4.2 12.6 1.0 O4 F:OXL1582 4.2 26.1 1.0 ND2 F:ASN467 4.2 19.6 1.0 CE F:LYS183 4.2 8.6 1.0 NH2 F:ARG165 4.5 14.9 1.0 CB F:ASP279 4.5 14.4 1.0 CB F:ASP256 4.5 13.1 1.0 C5N F:NAP1581 4.6 12.5 1.0 CA F:ASP256 4.6 13.1 1.0 OD2 F:ASP278 4.7 19.7 1.0 CG F:GLU255 4.8 16.5 1.0 CZ F:ARG165 4.8 15.1 1.0 CL F:CL1586 4.8 40.4 1.0 C4N F:NAP1581 4.9 12.6 1.0 CB F:GLU255 5.0 13.1 1.0 CD2 F:LEU167 5.0 1.0 1.0 CA F:ASP279 5.0 14.0 1.0 C F:GLU255 5.0 12.5 1.0

Manganese binding site 7 out of 16 in the Malic Enzyme From Pigeon Liver


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 7 of Malic Enzyme From Pigeon Liver within 5.0Å range: probe atom residue distance (Å) B Occ G:Mn1583 b:16.2 occ:1.00 OE2 G:GLU255 2.2 7.2 1.0 OD2 G:ASP256 2.2 16.7 1.0 O3 G:OXL1582 2.3 25.0 1.0 OD1 G:ASP279 2.3 14.7 1.0 O2 G:OXL1582 2.5 32.2 1.0 C1 G:OXL1582 3.0 28.4 1.0 C2 G:OXL1582 3.1 30.5 1.0 CD G:GLU255 3.2 9.8 1.0 CG G:ASP256 3.3 15.8 1.0 CG G:ASP279 3.3 16.5 1.0 CG G:GLU255 3.6 11.2 1.0 OD2 G:ASP279 3.8 18.4 1.0 OD1 G:ASP256 3.8 17.1 1.0 NZ G:LYS183 4.0 13.1 1.0 ND2 G:ASN467 4.0 24.4 1.0 O1 G:OXL1582 4.1 28.4 1.0 CE G:LYS183 4.2 11.5 1.0 N G:ASP256 4.2 14.3 1.0 O4 G:OXL1582 4.3 30.5 1.0 NH1 G:ARG165 4.3 13.9 1.0 OE1 G:GLU255 4.3 11.3 1.0 NH2 G:ARG165 4.4 13.0 1.0 CB G:ASP256 4.5 15.0 1.0 CB G:ASP279 4.6 15.1 1.0 OD2 G:ASP278 4.6 18.9 1.0 CA G:ASP256 4.7 15.6 1.0 C5N G:NAP1581 4.7 24.1 1.0 CZ G:ARG165 4.8 14.2 1.0 O G:HOH2065 4.9 20.4 1.0 CA G:ASP279 4.9 13.7 1.0 CB G:GLU255 4.9 11.8 1.0 N G:ASP279 4.9 14.7 1.0

Manganese binding site 8 out of 16 in the Malic Enzyme From Pigeon Liver


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 8 of Malic Enzyme From Pigeon Liver within 5.0Å range: probe atom residue distance (Å) B Occ H:Mn1583 b:15.7 occ:1.00 OD1 H:ASP256 2.3 16.2 1.0 O3 H:OXL1582 2.3 17.9 1.0 OE2 H:GLU255 2.3 24.8 1.0 O2 H:OXL1582 2.4 21.9 1.0 OD1 H:ASP279 2.4 15.4 1.0 OE1 H:GLU255 3.0 21.4 1.0 CD H:GLU255 3.0 20.6 1.0 C1 H:OXL1582 3.0 21.7 1.0 C2 H:OXL1582 3.0 22.3 1.0 CG H:ASP256 3.1 15.2 1.0 CG H:ASP279 3.3 14.6 1.0 OD2 H:ASP256 3.4 17.6 1.0 OD2 H:ASP279 3.5 16.6 1.0 NZ H:LYS183 3.7 13.5 1.0 ND2 H:ASN467 4.1 19.9 1.0 N H:ASP256 4.2 12.9 1.0 O1 H:OXL1582 4.2 22.2 1.0 NH1 H:ARG165 4.3 12.7 1.0 O4 H:OXL1582 4.3 25.4 1.0 CE H:LYS183 4.4 11.0 1.0 CB H:ASP256 4.4 13.3 1.0 NH2 H:ARG165 4.4 14.1 1.0 CG H:GLU255 4.4 18.2 1.0 C5N H:NAP1581 4.6 19.0 1.0 CB H:ASP279 4.6 14.0 1.0 CA H:ASP256 4.6 14.3 1.0 CZ H:ARG165 4.8 13.4 1.0 CB H:GLU255 4.9 14.0 1.0 OD2 H:ASP278 4.9 20.6 1.0 CA H:ASP279 5.0 14.1 1.0 CG2 H:ILE179 5.0 11.5 1.0

Manganese binding site 9 out of 16 in the Malic Enzyme From Pigeon Liver


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 9 of Malic Enzyme From Pigeon Liver within 5.0Å range: probe atom residue distance (Å) B Occ I:Mn1583 b:8.6 occ:1.00 O3 I:OXL1582 2.2 21.2 1.0 OD1 I:ASP279 2.2 14.2 1.0 OE2 I:GLU255 2.3 11.4 1.0 OD2 I:ASP256 2.3 15.3 1.0 O2 I:OXL1582 2.3 23.4 1.0 C1 I:OXL1582 2.9 24.0 1.0 C2 I:OXL1582 2.9 25.3 1.0 CG I:ASP279 3.0 13.2 1.0 OD2 I:ASP279 3.0 15.0 1.0 CD I:GLU255 3.3 10.8 1.0 CG I:ASP256 3.4 13.8 1.0 NZ I:LYS183 3.7 8.6 1.0 CG I:GLU255 3.7 10.1 1.0 OD1 I:ASP256 4.0 14.3 1.0 O1 I:OXL1582 4.0 23.5 1.0 CE I:LYS183 4.1 10.8 1.0 N I:ASP256 4.2 12.2 1.0 O4 I:OXL1582 4.2 27.3 1.0 NH2 I:ARG165 4.3 8.6 1.0 CB I:ASP279 4.3 13.1 1.0 OD1 I:ASN467 4.4 20.3 1.0 OE1 I:GLU255 4.4 10.8 1.0 NH1 I:ARG165 4.5 7.8 1.0 C5N I:NAP1581 4.5 11.4 1.0 OD2 I:ASP278 4.6 12.4 1.0 CB I:ASP256 4.6 12.3 1.0 CA I:ASP256 4.7 11.8 1.0 CZ I:ARG165 4.8 9.8 1.0 CA I:ASP279 4.9 12.6 1.0 CD2 I:LEU167 4.9 3.7 1.0 C4N I:NAP1581 4.9 10.9 1.0 CB I:GLU255 5.0 9.4 1.0 N I:ASP279 5.0 12.6 1.0 O I:HOH2019 5.0 6.4 1.0

Manganese binding site 10 out of 16 in the Malic Enzyme From Pigeon Liver


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 10 of Malic Enzyme From Pigeon Liver within 5.0Å range: probe atom residue distance (Å) B Occ J:Mn1583 b:12.1 occ:1.00 OD1 J:ASP279 2.1 14.1 1.0 OE1 J:GLU255 2.2 7.0 1.0 OD1 J:ASP256 2.3 3.9 1.0 O3 J:OXL1582 2.3 18.0 1.0 O2 J:OXL1582 2.3 19.7 1.0 O J:HOH2063 2.4 9.7 1.0 C2 J:OXL1582 2.9 22.1 1.0 C1 J:OXL1582 2.9 20.3 1.0 CG J:ASP279 3.1 14.6 1.0 CD J:GLU255 3.3 7.8 1.0 CG J:ASP256 3.3 7.6 1.0 OD2 J:ASP279 3.4 15.3 1.0 OD2 J:ASP256 3.7 9.3 1.0 CG J:GLU255 3.8 6.3 1.0 ND2 J:ASN467 4.1 18.8 1.0 NZ J:LYS183 4.1 13.2 1.0 O1 J:OXL1582 4.1 20.9 1.0 O4 J:OXL1582 4.1 24.4 1.0 NH1 J:ARG165 4.2 12.8 1.0 NH2 J:ARG165 4.2 9.4 1.0 CE J:LYS183 4.3 13.3 1.0 N J:ASP256 4.3 10.4 1.0 OE2 J:GLU255 4.4 10.3 1.0 C5N J:NAP1581 4.4 17.4 1.0 CB J:ASP279 4.5 14.5 1.0 CB J:ASP256 4.6 8.0 1.0 CZ J:ARG165 4.6 12.8 1.0 CD2 J:LEU167 4.7 8.1 1.0 CA J:ASP256 4.8 10.9 1.0 CA J:ASP279 4.8 13.9 1.0 C6N J:NAP1581 4.9 16.7 1.0 C4N J:NAP1581 4.9 15.3 1.0

Z.Yang, H.Zhang, H.-C.Huang, C.-C.Kuo, L.-C.Tsai, H.S.Yuan, W.-Y.Chou, G.-G.Chang, L.Tong. Structural Studies of the Pigeon Cytosolic Nadp+ -Dependent Malic Enzyme Protein Sci. V. 11 332 2002.
ISSN: ISSN 0961-8368
PubMed: 11790843
DOI: 10.1110/PS.38002