Manganese in the structure of Crystal Structure of Human M340H-Beta-1,4-Galactosyltransferase-1 (M340H-B4GAL-T1) in Complex With Glcnac-BETA1,6-Gal-BETA1,4-Glc-Beta (pdb 4eea)
The binding sites of Manganese atom in the structure of Crystal Structure of Human M340H-Beta-1,4-Galactosyltransferase-1 (M340H-B4GAL-T1) in Complex With Glcnac-BETA1,6-Gal-BETA1,4-Glc-Beta (pdb code 4eea). This binding sites where shown with 5.0 Angstroms radius around Manganese atom. The 4eea structure was solved by B.RAMAKRISHNAN, P.K.QASBA, with X-Ray Crystallography technique, brief refinement statistics is given in the table below:
Resolution (A) | 40.5-2.0 | Space group | C2221 | a (A) | 107.322 | b (A) | 196.204 | c (A) | 143.594 | alpha (°) | 90.00 | beta (°) | 90.00 | gamma (°) | 90.00 | Rfactor (%) | 20 | Rfree (%) | 24 |
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Manganese Binding Sites:Manganese binding site 1 out of 3 in 4eea
|  Click to enlarge |  Click to enlarge | Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Manganese in the PDB 4eea. 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: Arg187, A: Asp250, A: His340, A: Ile341, A: His343, A: Udp404, A: Hoh691, | conact list:
Atom | Atom | Distance (A) | Mn | CZ A:Arg187 | 4.72 | Mn | NH2 A:Arg187 | 4.12 | Mn | NH1 A:Arg187 | 4.35 | Mn | CB A:Asp250 | 4.26 | Mn | OD2 A:Asp250 | 2.22 | Mn | OD1 A:Asp250 | 3.57 | Mn | CG A:Asp250 | 3.12 | Mn | NE2 A:His340 | 2.41 | Mn | ND1 A:His340 | 4.50 | Mn | CD2 A:His340 | 3.39 | Mn | CE1 A:His340 | 3.36 | Mn | CG A:His340 | 4.54 | Mn | O A:Ile341 | 4.86 | Mn | NE2 A:His343 | 2.29 | Mn | ND1 A:His343 | 4.37 | Mn | CD2 A:His343 | 3.23 | Mn | CE1 A:His343 | 3.27 | Mn | CG A:His343 | 4.39 | Mn | O3B A:Udp404 | 2.36 | Mn | C3' A:Udp404 | 4.87 | Mn | PA A:Udp404 | 3.43 | Mn | O2A A:Udp404 | 4.22 | Mn | O1B A:Udp404 | 3.67 | Mn | PB A:Udp404 | 2.38 | Mn | O3' A:Udp404 | 4.18 | Mn | O5' A:Udp404 | 4.72 | Mn | O2B A:Udp404 | 1.81 | Mn | O3A A:Udp404 | 3.26 | Mn | O1A A:Udp404 | 2.45 | Mn | O A:Hoh691 | 4.92 |
| interactive model:
| Manganese binding site 2 out of 3 in 4eea
|  Click to enlarge |  Click to enlarge | Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Manganese in the PDB 4eea. 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: Arg187, B: Asp250, B: Lys275, B: His340, B: Ile341, B: His343, B: Udp404, B: Hoh535, B: Hoh589, B: Hoh615, | conact list:
Atom | Atom | Distance (A) | Mn | CZ B:Arg187 | 4.70 | Mn | NH2 B:Arg187 | 4.08 | Mn | NH1 B:Arg187 | 4.44 | Mn | CB B:Asp250 | 4.32 | Mn | OD2 B:Asp250 | 2.31 | Mn | OD1 B:Asp250 | 3.55 | Mn | CG B:Asp250 | 3.15 | Mn | NZ B:Lys275 | 4.57 | Mn | NE2 B:His340 | 2.28 | Mn | ND1 B:His340 | 4.38 | Mn | CD2 B:His340 | 3.25 | Mn | CE1 B:His340 | 3.26 | Mn | CG B:His340 | 4.41 | Mn | O B:Ile341 | 4.87 | Mn | NE2 B:His343 | 2.31 | Mn | ND1 B:His343 | 4.42 | Mn | CD2 B:His343 | 3.24 | Mn | CE1 B:His343 | 3.32 | Mn | CG B:His343 | 4.42 | Mn | O3B B:Udp404 | 2.45 | Mn | PA B:Udp404 | 3.43 | Mn | O2A B:Udp404 | 4.21 | Mn | O1B B:Udp404 | 4.64 | Mn | PB B:Udp404 | 3.30 | Mn | O3' B:Udp404 | 4.33 | Mn | O5' B:Udp404 | 4.83 | Mn | O2B B:Udp404 | 3.85 | Mn | O3A B:Udp404 | 3.26 | Mn | O1A B:Udp404 | 2.39 | Mn | O B:Hoh535 | 3.39 | Mn | O B:Hoh589 | 4.98 | Mn | O B:Hoh615 | 4.32 |
| interactive model:
| Manganese binding site 3 out of 3 in 4eea
|  Click to enlarge |  Click to enlarge | Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Manganese in the PDB 4eea. 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: C: Arg187, C: Asp250, C: Lys275, C: His340, C: Ile341, C: His343, C: Udp404, C: Hoh587, | conact list:
Atom | Atom | Distance (A) | Mn | CZ C:Arg187 | 4.89 | Mn | NH2 C:Arg187 | 4.22 | Mn | NH1 C:Arg187 | 4.60 | Mn | CB C:Asp250 | 4.46 | Mn | OD2 C:Asp250 | 2.32 | Mn | OD1 C:Asp250 | 3.56 | Mn | CG C:Asp250 | 3.22 | Mn | NZ C:Lys275 | 4.45 | Mn | NE2 C:His340 | 2.54 | Mn | ND1 C:His340 | 4.68 | Mn | CD2 C:His340 | 3.35 | Mn | CE1 C:His340 | 3.62 | Mn | CG C:His340 | 4.59 | Mn | O C:Ile341 | 4.90 | Mn | NE2 C:His343 | 2.32 | Mn | ND1 C:His343 | 4.42 | Mn | CD2 C:His343 | 3.24 | Mn | CE1 C:His343 | 3.32 | Mn | CG C:His343 | 4.42 | Mn | O3B C:Udp404 | 2.43 | Mn | C3' C:Udp404 | 4.98 | Mn | PA C:Udp404 | 3.27 | Mn | O2A C:Udp404 | 3.54 | Mn | O1B C:Udp404 | 4.67 | Mn | PB C:Udp404 | 3.45 | Mn | O3' C:Udp404 | 4.35 | Mn | O5' C:Udp404 | 4.73 | Mn | O2B C:Udp404 | 4.10 | Mn | O3A C:Udp404 | 3.57 | Mn | O1A C:Udp404 | 2.34 | Mn | O C:Hoh587 | 2.93 |
| interactive model:
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