Manganese in PDB 1jmb: Crystal Structure of Four-Helix Bundle Model

The structure of Crystal Structure of Four-Helix Bundle Model, PDB code: 1jmb was solved by L.Di Costanzo, S.Geremia, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 2.20
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	37.121, 112.451, 79.877, 90.00, 90.00, 90.00
R / Rfree (%)	24.7 / 31.8

The binding sites of Manganese atom in the Crystal Structure of Four-Helix Bundle Model (pdb code 1jmb). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 3 binding sites of Manganese where determined in the Crystal Structure of Four-Helix Bundle Model, PDB code: 1jmb:
Jump to Manganese binding site number: 1; 2; 3;

Manganese binding site 1 out of 3 in the Crystal Structure of Four-Helix Bundle Model


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 Four-Helix Bundle Model within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn401 b:33.2 occ:1.00 OE1 A:GLU36 2.1 27.8 1.0 ND1 A:HIS39 2.2 34.0 1.0 OE1 A:GLU10 2.2 33.3 1.0 OE2 A:GLU10 2.3 34.5 1.0 O A:DMS302 2.4 33.9 0.5 CD A:GLU10 2.6 34.5 1.0 CD A:GLU36 3.0 31.6 1.0 CG A:HIS39 3.2 33.0 1.0 CE1 A:HIS39 3.2 40.9 1.0 OE2 A:GLU36 3.4 25.5 1.0 CB A:HIS39 3.5 32.4 1.0 S A:DMS302 3.7 30.0 0.5 C2 A:DMS302 3.7 37.7 0.5 CG A:GLU10 4.1 38.9 1.0 CA A:GLU36 4.2 30.8 1.0 CG A:GLU36 4.3 26.0 1.0 NE2 A:HIS39 4.3 32.8 1.0 CD2 A:HIS39 4.3 36.2 1.0 CB A:GLU36 4.6 26.7 1.0 N A:GLU36 4.8 28.6 1.0 CB A:GLU10 4.9 41.2 1.0 CA A:HIS39 5.0 36.3 1.0

Manganese binding site 2 out of 3 in the Crystal Structure of Four-Helix Bundle Model


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 Four-Helix Bundle Model within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn402 b:22.8 occ:1.00 OE1 B:GLU10 1.9 28.6 1.0 OE2 C:GLU36 2.0 14.0 1.0 OE1 B:GLU36 2.2 26.2 1.0 ND1 B:HIS39 2.2 30.8 1.0 OE2 B:GLU10 2.5 32.5 1.0 O B:DMS301 2.5 29.9 0.5 CD B:GLU10 2.6 27.6 1.0 O B:DMS301 2.6 29.1 0.5 CD C:GLU36 3.0 21.4 1.0 CE1 B:HIS39 3.1 35.1 1.0 CD B:GLU36 3.2 23.2 1.0 CG B:HIS39 3.3 24.5 1.0 S B:DMS301 3.4 28.3 0.5 OE1 C:GLU36 3.4 22.0 1.0 S B:DMS301 3.5 26.5 0.5 CB B:HIS39 3.7 21.2 1.0 OE2 B:GLU36 3.7 12.2 1.0 C1 B:DMS301 3.7 26.6 0.5 MN C:MN403 3.8 25.4 1.0 C2 B:DMS301 3.8 25.3 0.5 CG B:GLU10 4.1 17.5 1.0 NE2 B:HIS39 4.3 22.1 1.0 CD2 B:HIS39 4.4 26.1 1.0 CG C:GLU36 4.4 17.6 1.0 CA B:GLU36 4.4 23.6 1.0 CE1 C:HIS39 4.5 30.7 1.0 CG B:GLU36 4.5 18.5 1.0 CG2 C:ILE32 4.5 22.6 1.0 CB B:GLU36 4.6 27.3 1.0 CE1 C:TYR17 4.7 28.7 1.0 ND1 C:HIS39 4.8 27.5 1.0 OH C:TYR17 4.8 23.7 1.0 C1 B:DMS301 4.9 23.3 0.5 OE1 C:GLU10 5.0 28.3 1.0 CB B:GLU10 5.0 25.7 1.0 N B:GLU36 5.0 21.4 1.0

Manganese binding site 3 out of 3 in the Crystal Structure of Four-Helix Bundle Model


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 Four-Helix Bundle Model within 5.0Å range: probe atom residue distance (Å) B Occ C:Mn403 b:25.4 occ:1.00 ND1 C:HIS39 2.0 27.5 1.0 OE2 B:GLU36 2.0 12.2 1.0 OE1 C:GLU10 2.0 28.3 1.0 OE1 C:GLU36 2.1 22.0 1.0 OE2 C:GLU10 2.4 26.8 1.0 CD C:GLU10 2.5 29.6 1.0 O B:DMS301 2.6 29.9 0.5 O B:DMS301 2.7 29.1 0.5 CE1 C:HIS39 2.8 30.7 1.0 CD B:GLU36 2.9 23.2 1.0 CG C:HIS39 3.1 23.3 1.0 CD C:GLU36 3.2 21.4 1.0 OE1 B:GLU36 3.3 26.2 1.0 S B:DMS301 3.5 28.3 0.5 CB C:HIS39 3.6 20.2 1.0 OE2 C:GLU36 3.7 14.0 1.0 S B:DMS301 3.8 26.5 0.5 MN B:MN402 3.8 22.8 1.0 C1 B:DMS301 3.9 23.3 0.5 NE2 C:HIS39 3.9 21.6 1.0 C2 B:DMS301 4.0 24.1 0.5 CG C:GLU10 4.0 32.0 1.0 CD2 C:HIS39 4.1 23.2 1.0 CA C:GLU36 4.2 21.2 1.0 CG B:GLU36 4.2 18.5 1.0 CG2 B:ILE32 4.3 20.9 1.0 OH B:TYR17 4.4 27.4 1.0 CG C:GLU36 4.5 17.6 1.0 CB C:GLU36 4.5 14.5 1.0 CE1 B:TYR17 4.7 24.3 1.0 CB C:GLU10 4.9 32.4 1.0 N C:GLU36 4.9 27.5 1.0 O C:GLU36 5.0 27.6 1.0 O C:ASP35 5.0 30.0 1.0

L.Di Costanzo, H.Wade, S.Geremia, L.Randaccio, V.Pavone, W.F.Degrado, A.Lombardi. Toward the De Novo Design of A Catalytically Active Helix Bundle: A Substrate-Accessible Carboxylate-Bridged Dinuclear Metal Center. J.Am.Chem.Soc. V. 123 12749 2001.
ISSN: ISSN 0002-7863
PubMed: 11749531
DOI: 10.1021/JA010506X