Manganese in the structure of Crystal Structure of Human Arginase I in Complex With 2- Aminohomohistidine (pdb 3mfv)
The binding sites of Manganese atom in the structure of Crystal Structure of Human Arginase I in Complex With 2- Aminohomohistidine (pdb code 3mfv). This binding sites where shown with 5.0 Angstroms radius around Manganese atom. The 3mfv structure was solved by L.DI COSTANZO, D.W.CHRISTIANSON, with X-Ray Crystallography technique, brief refinement statistics is given in the table below:
Resolution (A) | 50.0-1.9 | Space group | P3 | a (A) | 90.660 | b (A) | 90.660 | c (A) | 69.707 | alpha (°) | 90.00 | beta (°) | 90.00 | gamma (°) | 120.00 | Rfactor (%) | 14.1 | Rfree (%) | 19 |
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Manganese Binding Sites:Manganese binding site 1 out of 4 in 3mfv
|  Click to enlarge |  Click to enlarge | Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Manganese in the PDB 3mfv. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Manganese atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: A: Asp124, A: Ala125, A: His126, A: Asp128, A: Asp232, A: Asp234, A: Thr246, A: Mn615, A: Z700, A: Hoh400, | conact list:
Atom | Atom | Distance (A) | Mn | CB A:Asp124 | 4.31 | Mn | OD2 A:Asp124 | 3.25 | Mn | C A:Asp124 | 4.71 | Mn | OD1 A:Asp124 | 2.03 | Mn | CG A:Asp124 | 2.96 | Mn | CA A:Asp124 | 4.65 | Mn | N A:Ala125 | 3.90 | Mn | C A:Ala125 | 4.63 | Mn | CB A:Ala125 | 4.47 | Mn | CA A:Ala125 | 4.58 | Mn | NE2 A:His126 | 4.08 | Mn | N A:His126 | 3.90 | Mn | CB A:His126 | 3.96 | Mn | ND1 A:His126 | 2.17 | Mn | CD2 A:His126 | 4.36 | Mn | CE1 A:His126 | 2.84 | Mn | CG A:His126 | 3.40 | Mn | CA A:His126 | 4.55 | Mn | OD2 A:Asp128 | 4.98 | Mn | OD1 A:Asp128 | 4.77 | Mn | CB A:Asp232 | 4.15 | Mn | OD2 A:Asp232 | 2.15 | Mn | OD1 A:Asp232 | 3.88 | Mn | CG A:Asp232 | 3.19 | Mn | CB A:Asp234 | 4.18 | Mn | OD2 A:Asp234 | 2.31 | Mn | C A:Asp234 | 4.99 | Mn | OD1 A:Asp234 | 2.35 | Mn | CG A:Asp234 | 2.66 | Mn | OG1 A:Thr246 | 4.27 | Mn | MN A:Mn615 | 3.45 | Mn | C5 A:Z700 | 4.44 | Mn | N3 A:Z700 | 3.42 | Mn | N2 A:Z700 | 4.12 | Mn | C4 A:Z700 | 3.21 | Mn | C3 A:Z700 | 4.76 | Mn | N4 A:Z700 | 2.86 | Mn | O A:Hoh400 | 4.81 |
| interactive model:
| Manganese binding site 2 out of 4 in 3mfv
|  Click to enlarge |  Click to enlarge | Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Manganese in the PDB 3mfv. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Manganese atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: A: His101, A: Trp122, A: Asp124, A: His126, A: Asp128, A: His141, A: Asp232, A: Glu277, A: Mn614, A: Z700, | conact list:
Atom | Atom | Distance (A) | Mn | NE2 A:His101 | 4.39 | Mn | CB A:His101 | 3.38 | Mn | ND1 A:His101 | 2.30 | Mn | CD2 A:His101 | 4.36 | Mn | CE1 A:His101 | 3.31 | Mn | CG A:His101 | 3.19 | Mn | CA A:His101 | 4.90 | Mn | CZ2 A:Trp122 | 4.57 | Mn | CE2 A:Trp122 | 4.82 | Mn | NE1 A:Trp122 | 4.35 | Mn | CB A:Asp124 | 4.37 | Mn | OD2 A:Asp124 | 2.02 | Mn | OD1 A:Asp124 | 3.55 | Mn | CG A:Asp124 | 3.11 | Mn | ND1 A:His126 | 4.88 | Mn | CB A:Asp128 | 4.40 | Mn | OD2 A:Asp128 | 2.13 | Mn | OD1 A:Asp128 | 3.48 | Mn | CG A:Asp128 | 3.11 | Mn | O A:His141 | 4.21 | Mn | CB A:Asp232 | 3.74 | Mn | OD2 A:Asp232 | 2.58 | Mn | OD1 A:Asp232 | 4.47 | Mn | CG A:Asp232 | 3.43 | Mn | OE2 A:Glu277 | 4.49 | Mn | CG A:Glu277 | 4.67 | Mn | MN A:Mn614 | 3.45 | Mn | N3 A:Z700 | 4.62 | Mn | N2 A:Z700 | 3.74 | Mn | C4 A:Z700 | 3.38 | Mn | N4 A:Z700 | 2.35 |
| interactive model:
| Manganese binding site 3 out of 4 in 3mfv
|  Click to enlarge |  Click to enlarge | Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Manganese in the PDB 3mfv. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Manganese atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: B: Asp124, B: Ala125, B: His126, B: Asp128, B: Asp232, B: Asp234, B: Thr246, B: Glu277, B: Mn615, B: Z70323, B: Hoh331, | conact list:
Atom | Atom | Distance (A) | Mn | CB B:Asp124 | 4.50 | Mn | OD2 B:Asp124 | 3.22 | Mn | OD1 B:Asp124 | 2.27 | Mn | CG B:Asp124 | 3.08 | Mn | CA B:Asp124 | 4.94 | Mn | N B:Ala125 | 4.31 | Mn | C B:Ala125 | 4.96 | Mn | CB B:Ala125 | 4.91 | Mn | NE2 B:His126 | 4.22 | Mn | N B:His126 | 4.12 | Mn | CB B:His126 | 3.90 | Mn | ND1 B:His126 | 2.26 | Mn | CD2 B:His126 | 4.43 | Mn | CE1 B:His126 | 3.01 | Mn | CG B:His126 | 3.41 | Mn | CA B:His126 | 4.63 | Mn | OD2 B:Asp128 | 4.86 | Mn | OD1 B:Asp128 | 4.71 | Mn | CB B:Asp232 | 3.97 | Mn | OD2 B:Asp232 | 2.11 | Mn | OD1 B:Asp232 | 3.55 | Mn | CG B:Asp232 | 2.98 | Mn | CB B:Asp234 | 4.06 | Mn | OD2 B:Asp234 | 2.40 | Mn | C B:Asp234 | 4.99 | Mn | OD1 B:Asp234 | 2.08 | Mn | CG B:Asp234 | 2.55 | Mn | CA B:Asp234 | 4.98 | Mn | OG1 B:Thr246 | 4.40 | Mn | CG B:Glu277 | 4.99 | Mn | MN B:Mn615 | 3.39 | Mn | C5 B:Z70323 | 4.36 | Mn | N3 B:Z70323 | 3.32 | Mn | N2 B:Z70323 | 4.01 | Mn | C4 B:Z70323 | 3.07 | Mn | C3 B:Z70323 | 4.68 | Mn | N4 B:Z70323 | 2.69 | Mn | O B:Hoh331 | 4.85 |
| interactive model:
| Manganese binding site 4 out of 4 in 3mfv
|  Click to enlarge |  Click to enlarge | Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Manganese in the PDB 3mfv. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Manganese atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: B: His101, B: Trp122, B: Asp124, B: Asp128, B: His141, B: Asp232, B: Glu277, B: Mn614, B: Z70323, | conact list:
Atom | Atom | Distance (A) | Mn | NE2 B:His101 | 4.47 | Mn | CB B:His101 | 3.27 | Mn | ND1 B:His101 | 2.37 | Mn | CD2 B:His101 | 4.37 | Mn | CE1 B:His101 | 3.43 | Mn | CG B:His101 | 3.17 | Mn | CA B:His101 | 4.80 | Mn | CZ2 B:Trp122 | 4.32 | Mn | CE2 B:Trp122 | 4.65 | Mn | NE1 B:Trp122 | 4.27 | Mn | CB B:Asp124 | 4.64 | Mn | OD2 B:Asp124 | 2.29 | Mn | OD1 B:Asp124 | 3.82 | Mn | CG B:Asp124 | 3.39 | Mn | CB B:Asp128 | 4.37 | Mn | OD2 B:Asp128 | 2.08 | Mn | OD1 B:Asp128 | 3.49 | Mn | CG B:Asp128 | 3.08 | Mn | O B:His141 | 4.15 | Mn | CB B:Asp232 | 3.82 | Mn | OD2 B:Asp232 | 2.64 | Mn | OD1 B:Asp232 | 4.73 | Mn | CG B:Asp232 | 3.59 | Mn | OE2 B:Glu277 | 4.88 | Mn | CG B:Glu277 | 4.75 | Mn | MN B:Mn614 | 3.39 | Mn | N3 B:Z70323 | 4.76 | Mn | N2 B:Z70323 | 3.77 | Mn | C4 B:Z70323 | 3.50 | Mn | N4 B:Z70323 | 2.57 |
| interactive model:
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