Manganese in PDB 1vkm: Crystal Structure of An Indigoidine Synthase A (Idga)-Like Protein (TM1464) From Thermotoga Maritima MSB8 at 1.90 A Resolution

The structure of Crystal Structure of An Indigoidine Synthase A (Idga)-Like Protein (TM1464) From Thermotoga Maritima MSB8 at 1.90 A Resolution, PDB code: 1vkm was solved by Joint Center For Structural Genomics (Jcsg), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	75.23 / 1.90
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	91.958, 130.799, 138.750, 90.00, 90.00, 90.00
R / Rfree (%)	15.4 / 20

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

Binding sites:

The binding sites of Manganese atom in the Crystal Structure of An Indigoidine Synthase A (Idga)-Like Protein (TM1464) From Thermotoga Maritima MSB8 at 1.90 A Resolution (pdb code 1vkm). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 16 binding sites of Manganese where determined in the Crystal Structure of An Indigoidine Synthase A (Idga)-Like Protein (TM1464) From Thermotoga Maritima MSB8 at 1.90 A Resolution, PDB code: 1vkm:
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 Crystal Structure of An Indigoidine Synthase A (Idga)-Like Protein (TM1464) From Thermotoga Maritima MSB8 at 1.90 A Resolution


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Crystal Structure of An Indigoidine Synthase A (Idga)-Like Protein (TM1464) From Thermotoga Maritima MSB8 at 1.90 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn300 b:22.9 occ:1.00 OE2 C:GLU206 2.0 23.7 1.0 NE2 A:HIS-2 2.1 21.2 1.0 O C:GLU204 2.2 19.3 1.0 NE2 A:HIS-4 2.2 20.5 1.0 O C:HOH612 2.3 16.7 1.0 NE2 E:HIS-5 2.5 13.7 1.0 CE1 A:HIS-2 3.0 31.0 1.0 CD C:GLU206 3.0 27.1 1.0 CE1 A:HIS-4 3.2 26.8 1.0 CD2 A:HIS-2 3.2 21.7 1.0 CD2 A:HIS-4 3.2 23.3 1.0 CD2 E:HIS-5 3.3 14.2 1.0 C C:GLU204 3.4 18.4 1.0 OE1 C:GLU206 3.4 21.6 1.0 CE1 E:HIS-5 3.5 20.1 1.0 CA C:GLU204 4.0 20.4 1.0 O C:HOH623 4.1 20.4 1.0 ND1 A:HIS-2 4.2 34.2 1.0 CG A:HIS-2 4.3 28.9 1.0 ND1 A:HIS-4 4.3 22.8 1.0 CG C:GLU206 4.3 23.2 1.0 CG A:HIS-4 4.4 23.4 1.0 N C:MSE205 4.4 18.5 1.0 CG E:HIS-5 4.5 12.1 1.0 ND1 E:HIS-5 4.6 13.2 1.0 CA C:MSE205 4.6 20.8 1.0 O A:HOH675 4.6 25.0 1.0 CB C:GLU204 4.7 22.7 1.0 O C:LYS203 4.8 23.1 1.0 N C:GLU206 4.9 21.2 1.0

Manganese binding site 2 out of 16 in the Crystal Structure of An Indigoidine Synthase A (Idga)-Like Protein (TM1464) From Thermotoga Maritima MSB8 at 1.90 A Resolution


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Crystal Structure of An Indigoidine Synthase A (Idga)-Like Protein (TM1464) From Thermotoga Maritima MSB8 at 1.90 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn400 b:22.3 occ:1.00 O A:HOH611 2.2 13.9 1.0 OD1 A:ASP126 2.2 20.2 1.0 O A:HOH602 2.3 10.4 1.0 O A:HOH605 2.3 12.3 1.0 O C:HOH604 2.3 12.8 1.0 O A:HOH606 2.3 12.8 1.0 CG A:ASP126 3.2 22.2 1.0 OD2 A:ASP126 3.4 23.4 1.0 OE1 C:GLU160 4.0 20.4 1.0 OE2 C:GLU160 4.0 25.4 1.0 O C:HOH603 4.0 12.5 1.0 O4P A:UNL600 4.0 25.2 1.0 O A:GLY241 4.2 23.6 1.0 NE2 A:HIS121 4.2 19.7 1.0 OE1 C:GLU157 4.2 22.1 1.0 CD C:GLU160 4.2 19.4 1.0 O A:HOH608 4.2 13.2 1.0 C A:GLY241 4.4 26.6 1.0 CD2 A:HIS121 4.4 23.7 1.0 O2P A:UNL600 4.4 29.3 1.0 O A:HOH610 4.6 13.7 1.0 CB A:ASP126 4.6 22.5 1.0 O A:VAL127 4.6 21.8 1.0 CA A:GLY241 4.6 23.8 1.0 N A:VAL127 4.6 19.9 1.0 C A:VAL127 4.7 20.4 1.0 O C:HOH611 4.8 16.6 1.0 P A:UNL600 4.8 29.2 1.0 C A:ASP126 4.9 21.0 1.0 CA A:ASP126 4.9 19.6 1.0 N A:SER128 4.9 21.8 1.0

Manganese binding site 3 out of 16 in the Crystal Structure of An Indigoidine Synthase A (Idga)-Like Protein (TM1464) From Thermotoga Maritima MSB8 at 1.90 A Resolution


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Crystal Structure of An Indigoidine Synthase A (Idga)-Like Protein (TM1464) From Thermotoga Maritima MSB8 at 1.90 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn401 b:49.7 occ:1.00 OE1 A:GLU229 2.2 25.8 1.0 O A:HOH808 2.5 42.5 1.0 O A:HOH811 2.6 43.0 1.0 O A:HOH818 2.6 45.0 1.0 CD A:GLU229 3.1 31.7 1.0 OE2 A:GLU229 3.4 30.2 1.0 CB A:ASP226 4.2 27.1 1.0 CA A:ASP226 4.2 26.5 1.0 NH1 A:ARG230 4.3 27.7 1.0 CG A:GLU229 4.4 24.5 1.0 N A:ASP226 4.7 23.6 1.0 NH2 A:ARG230 4.7 27.4 1.0 CB A:GLU229 4.7 20.1 1.0 CD2 A:HIS225 4.8 30.4 1.0 CZ A:ARG230 5.0 26.0 1.0

Manganese binding site 4 out of 16 in the Crystal Structure of An Indigoidine Synthase A (Idga)-Like Protein (TM1464) From Thermotoga Maritima MSB8 at 1.90 A Resolution


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Crystal Structure of An Indigoidine Synthase A (Idga)-Like Protein (TM1464) From Thermotoga Maritima MSB8 at 1.90 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn300 b:22.4 occ:1.00 OE2 A:GLU206 2.1 22.7 1.0 NE2 B:HIS-4 2.2 19.6 1.0 O A:GLU204 2.2 19.9 1.0 NE2 F:HIS-5 2.2 14.3 1.0 NE2 B:HIS-2 2.3 24.2 1.0 O A:HOH626 2.4 17.9 1.0 CD A:GLU206 3.1 24.6 1.0 CE1 B:HIS-2 3.1 23.1 1.0 CD2 B:HIS-4 3.2 20.1 1.0 CD2 F:HIS-5 3.2 21.4 1.0 CE1 B:HIS-4 3.2 23.0 1.0 CE1 F:HIS-5 3.2 21.6 1.0 CD2 B:HIS-2 3.3 26.1 1.0 C A:GLU204 3.4 20.8 1.0 OE1 A:GLU206 3.4 23.7 1.0 O A:HOH645 4.0 20.5 1.0 CA A:GLU204 4.1 20.0 1.0 ND1 B:HIS-2 4.3 28.9 1.0 ND1 F:HIS-5 4.3 15.5 1.0 ND1 B:HIS-4 4.3 19.1 1.0 CG F:HIS-5 4.3 20.3 1.0 CG B:HIS-4 4.3 16.4 1.0 CG B:HIS-2 4.4 23.2 1.0 CG A:GLU206 4.4 19.2 1.0 N A:MSE205 4.5 18.1 1.0 CA A:MSE205 4.7 19.5 1.0 O B:HOH626 4.7 23.8 1.0 CB A:GLU204 4.7 21.3 1.0 O A:LYS203 4.8 21.9 1.0

Manganese binding site 5 out of 16 in the Crystal Structure of An Indigoidine Synthase A (Idga)-Like Protein (TM1464) From Thermotoga Maritima MSB8 at 1.90 A Resolution


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 5 of Crystal Structure of An Indigoidine Synthase A (Idga)-Like Protein (TM1464) From Thermotoga Maritima MSB8 at 1.90 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn400 b:21.1 occ:1.00 O B:HOH609 2.1 17.7 1.0 OD1 B:ASP126 2.2 19.2 1.0 O A:HOH616 2.2 15.6 1.0 O A:HOH636 2.2 19.4 1.0 O B:HOH604 2.3 15.2 1.0 O B:HOH607 2.4 17.4 1.0 CG B:ASP126 3.1 21.8 1.0 OD2 B:ASP126 3.4 17.6 1.0 O A:HOH604 4.0 11.5 1.0 OE1 A:GLU160 4.0 23.2 1.0 OE2 A:GLU160 4.0 27.0 1.0 O4P B:UNL600 4.1 24.8 1.0 CD A:GLU160 4.2 25.3 1.0 OE1 A:GLU157 4.2 24.5 1.0 O B:GLY241 4.2 25.7 1.0 O B:HOH625 4.3 22.8 1.0 NE2 B:HIS121 4.3 23.0 1.0 O B:HOH605 4.3 16.5 1.0 C B:GLY241 4.5 23.8 1.0 O2P B:UNL600 4.5 28.6 1.0 CB B:ASP126 4.5 21.8 1.0 CD2 B:HIS121 4.5 23.8 1.0 O B:VAL127 4.6 21.0 1.0 N B:VAL127 4.7 18.7 1.0 P B:UNL600 4.7 29.3 1.0 C B:VAL127 4.8 20.3 1.0 CA B:GLY241 4.8 23.4 1.0 C B:ASP126 4.9 20.4 1.0 CA B:ASP126 4.9 19.4 1.0 O B:HOH615 4.9 18.9 1.0 N B:SER128 4.9 20.0 1.0

Manganese binding site 6 out of 16 in the Crystal Structure of An Indigoidine Synthase A (Idga)-Like Protein (TM1464) From Thermotoga Maritima MSB8 at 1.90 A Resolution


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 6 of Crystal Structure of An Indigoidine Synthase A (Idga)-Like Protein (TM1464) From Thermotoga Maritima MSB8 at 1.90 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ C:Mn300 b:23.1 occ:1.00 OE2 B:GLU206 2.2 24.9 1.0 NE2 C:HIS-4 2.2 22.0 1.0 NE2 C:HIS-2 2.2 22.9 1.0 O B:GLU204 2.3 20.3 1.0 NE2 D:HIS-5 2.3 18.7 1.0 O B:HOH614 2.4 18.8 1.0 CE1 C:HIS-2 3.1 32.6 1.0 CD B:GLU206 3.1 22.5 1.0 CD2 C:HIS-4 3.2 18.8 1.0 CE1 D:HIS-5 3.2 28.9 1.0 CE1 C:HIS-4 3.2 20.5 1.0 CD2 D:HIS-5 3.2 27.3 1.0 CD2 C:HIS-2 3.3 27.2 1.0 OE1 B:GLU206 3.4 23.0 1.0 C B:GLU204 3.4 18.9 1.0 CA B:GLU204 4.1 19.2 1.0 O B:HOH617 4.2 19.7 1.0 ND1 C:HIS-2 4.3 36.7 1.0 ND1 D:HIS-5 4.3 24.4 1.0 ND1 C:HIS-4 4.3 19.4 1.0 CG C:HIS-4 4.3 21.9 1.0 CG D:HIS-5 4.4 21.8 1.0 CG C:HIS-2 4.4 26.1 1.0 N B:MSE205 4.5 17.5 1.0 CG B:GLU206 4.5 22.0 1.0 O C:HOH669 4.6 29.3 1.0 CA B:MSE205 4.7 20.2 1.0 CB B:GLU204 4.8 17.9 1.0 O B:LYS203 4.8 22.3 1.0

Manganese binding site 7 out of 16 in the Crystal Structure of An Indigoidine Synthase A (Idga)-Like Protein (TM1464) From Thermotoga Maritima MSB8 at 1.90 A Resolution


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 7 of Crystal Structure of An Indigoidine Synthase A (Idga)-Like Protein (TM1464) From Thermotoga Maritima MSB8 at 1.90 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ C:Mn400 b:20.8 occ:1.00 O C:HOH614 2.1 17.1 1.0 OD1 C:ASP126 2.2 14.0 1.0 O B:HOH613 2.2 18.8 1.0 O C:HOH610 2.3 16.6 1.0 O C:HOH636 2.3 22.8 1.0 O C:HOH621 2.4 19.7 1.0 CG C:ASP126 3.1 23.1 1.0 OD2 C:ASP126 3.3 21.4 1.0 OE2 B:GLU160 3.9 23.9 1.0 O B:HOH611 4.0 18.1 1.0 O4P C:UNL600 4.1 24.8 1.0 OE1 B:GLU160 4.1 21.1 1.0 NE2 C:HIS121 4.2 24.4 1.0 CD B:GLU160 4.2 22.6 1.0 O C:GLY241 4.2 23.9 1.0 OE1 B:GLU157 4.3 22.8 1.0 O C:HOH629 4.3 21.1 1.0 CD2 C:HIS121 4.4 19.2 1.0 O2P C:UNL600 4.4 25.8 1.0 O C:HOH632 4.4 21.8 1.0 C C:GLY241 4.5 26.1 1.0 CB C:ASP126 4.5 19.5 1.0 O C:VAL127 4.6 19.5 1.0 N C:VAL127 4.6 20.1 1.0 CA C:GLY241 4.7 26.3 1.0 C C:VAL127 4.7 20.1 1.0 P C:UNL600 4.8 31.4 1.0 C C:ASP126 4.9 22.0 1.0 O C:HOH664 4.9 28.7 1.0 N C:SER128 4.9 19.7 1.0 CA C:ASP126 4.9 19.6 1.0

Manganese binding site 8 out of 16 in the Crystal Structure of An Indigoidine Synthase A (Idga)-Like Protein (TM1464) From Thermotoga Maritima MSB8 at 1.90 A Resolution


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 8 of Crystal Structure of An Indigoidine Synthase A (Idga)-Like Protein (TM1464) From Thermotoga Maritima MSB8 at 1.90 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ C:Mn401 b:36.1 occ:1.00 OE1 C:GLU68 2.1 27.9 1.0 O C:HOH716 2.1 37.6 1.0 O C:HOH722 2.2 38.1 1.0 OE2 C:GLU64 2.3 26.7 1.0 OE2 C:GLU65 2.3 33.2 1.0 O C:HOH686 2.6 32.0 1.0 CD C:GLU68 3.0 23.1 1.0 CD C:GLU64 3.2 26.7 1.0 CD C:GLU65 3.2 34.5 1.0 OE2 C:GLU68 3.4 34.3 1.0 OE1 C:GLU65 3.4 27.2 1.0 CG C:GLU64 3.4 27.8 1.0 O C:HOH734 4.1 41.0 1.0 NH2 C:ARG35 4.1 27.7 1.0 OE1 C:GLU64 4.4 22.5 1.0 CG C:GLU68 4.4 20.0 1.0 CG C:GLU65 4.6 25.1 1.0 CB C:GLU64 4.7 22.6 1.0

Manganese binding site 9 out of 16 in the Crystal Structure of An Indigoidine Synthase A (Idga)-Like Protein (TM1464) From Thermotoga Maritima MSB8 at 1.90 A Resolution


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 9 of Crystal Structure of An Indigoidine Synthase A (Idga)-Like Protein (TM1464) From Thermotoga Maritima MSB8 at 1.90 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ D:Mn300 b:23.3 occ:1.00 OE2 E:GLU206 2.1 23.3 1.0 O E:HOH618 2.2 18.1 1.0 NE2 D:HIS-2 2.2 25.4 1.0 O E:GLU204 2.2 17.0 1.0 NE2 D:HIS-4 2.3 18.2 1.0 NE2 C:HIS-5 2.3 15.8 1.0 CE1 D:HIS-2 3.1 31.4 1.0 CD E:GLU206 3.1 27.5 1.0 CD2 D:HIS-4 3.2 16.9 1.0 CD2 C:HIS-5 3.2 19.6 1.0 CE1 D:HIS-4 3.3 24.3 1.0 CD2 D:HIS-2 3.3 26.7 1.0 CE1 C:HIS-5 3.4 24.9 1.0 C E:GLU204 3.4 19.7 1.0 OE1 E:GLU206 3.5 20.7 1.0 CA E:GLU204 4.1 19.6 1.0 O C:HOH634 4.2 22.2 1.0 ND1 D:HIS-2 4.3 35.6 1.0 ND1 D:HIS-4 4.4 23.7 1.0 CG D:HIS-2 4.4 30.9 1.0 O D:HOH767 4.4 14.6 0.4 CG D:HIS-4 4.4 19.8 1.0 CG C:HIS-5 4.4 21.0 1.0 CG E:GLU206 4.4 28.0 1.0 ND1 C:HIS-5 4.4 15.8 1.0 N E:MSE205 4.4 17.6 1.0 O D:HOH767 4.5 11.5 0.6 CA E:MSE205 4.6 20.0 1.0 CB E:GLU204 4.8 22.1 1.0 O E:LYS203 4.8 21.6 1.0 N E:GLU206 4.9 20.0 1.0

Manganese binding site 10 out of 16 in the Crystal Structure of An Indigoidine Synthase A (Idga)-Like Protein (TM1464) From Thermotoga Maritima MSB8 at 1.90 A Resolution


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 10 of Crystal Structure of An Indigoidine Synthase A (Idga)-Like Protein (TM1464) From Thermotoga Maritima MSB8 at 1.90 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ D:Mn400 b:21.6 occ:1.00 O D:HOH609 2.1 11.8 1.0 O E:HOH604 2.1 10.3 1.0 OD1 D:ASP126 2.2 20.4 1.0 O E:HOH606 2.2 10.7 1.0 O D:HOH603 2.3 9.4 1.0 O D:HOH605 2.3 10.5 1.0 CG D:ASP126 3.2 21.9 1.0 OD2 D:ASP126 3.4 23.1 1.0 OE1 E:GLU160 4.0 20.7 1.0 OE2 E:GLU160 4.0 23.7 1.0 O E:HOH605 4.1 10.5 1.0 OE1 E:GLU157 4.1 25.7 1.0 CD E:GLU160 4.2 22.8 1.0 O4P D:UNL600 4.2 28.1 1.0 O D:GLY241 4.2 22.8 1.0 NE2 D:HIS121 4.2 23.7 1.0 O D:HOH621 4.4 16.8 1.0 CD2 D:HIS121 4.4 23.2 1.0 C D:GLY241 4.4 25.0 1.0 O D:HOH612 4.5 13.1 1.0 O2P D:UNL600 4.5 31.4 1.0 CB D:ASP126 4.5 22.9 1.0 O D:VAL127 4.6 19.9 1.0 N D:VAL127 4.6 22.1 1.0 CA D:GLY241 4.6 24.2 1.0 C D:VAL127 4.7 20.3 1.0 C D:ASP126 4.8 21.5 1.0 P D:UNL600 4.8 31.8 1.0 O E:HOH617 4.8 17.8 1.0 CA D:ASP126 4.9 20.4 1.0 N D:SER128 4.9 19.8 1.0

I.Levin, M.D.Miller, R.Schwarzenbacher, D.Mcmullan, P.Abdubek, E.Ambing, T.Biorac, J.Cambell, J.M.Canaves, H.J.Chiu, A.M.Deacon, M.Didonato, M.A.Elsliger, A.Godzik, C.Grittini, S.K.Grzechnik, J.Hale, E.Hampton, G.W.Han, J.Haugen, M.Hornsby, L.Jaroszewski, C.Karlak, H.E.Klock, E.Koesema, A.Kreusch, P.Kuhn, S.A.Lesley, A.Morse, K.Moy, E.Nigoghossian, J.Ouyang, R.Page, K.Quijano, R.Reyes, A.Robb, E.Sims, G.Spraggon, R.C.Stevens, H.Van Den Bedem, J.Velasquez, J.Vincent, X.Wang, B.West, G.Wolf, Q.Xu, O.Zagnitko, K.O.Hodgson, J.Wooley, I.A.Wilson. Crystal Structure of An Indigoidine Synthase A (Inda)-Like Protein (TM1464) From Thermotoga Maritima at 1.90 A Resolution Reveals A New Fold. Proteins V. 59 864 2005.
ISSN: ISSN 0887-3585
PubMed: 15822122
DOI: 10.1002/PROT.20420