Manganese in the structure of Human Beta 1,3-Glucuronyltransferase I (Glcat-I) in Complex With Udp and Gal-Gal(6-SO4)-Xyl(2-PO4)-O-Ser (pdb 3cu0)
The binding sites of Manganese atom in the structure of Human Beta 1,3-Glucuronyltransferase I (Glcat-I) in Complex With Udp and Gal-Gal(6-SO4)-Xyl(2-PO4)-O-Ser (pdb code 3cu0). This binding sites where shown with 5.0 Angstroms radius around Manganese atom. The 3cu0 structure was solved by Y.TONE, L.C.PEDERSEN, T.YAMAMOTO, H.KITAGAWA, J.NISHIHARA-SHIMIZU, J.TAMURA, M.NEGISHI, K.SUGAHARA, with X-Ray Crystallography technique, brief refinement statistics is given in the table below:
Resolution (A) | 23.6-1.9 | Space group | P1211 | a (A) | 57.047 | b (A) | 48.399 | c (A) | 103.708 | alpha (°) | 90.00 | beta (°) | 92.40 | gamma (°) | 90.00 | Rfactor (%) | 21 | Rfree (%) | 23.4 |
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Manganese Binding Sites:Manganese binding site 1 out of 2 in 3cu0
|  Click to enlarge |  Click to enlarge | Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Manganese in the PDB 3cu0. 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: Asp194, A: Asp196, A: Asn197, A: His308, A: Thr309, A: Arg310, A: Udp501, A: Hoh504, A: Hoh505, A: Hoh522, A: Hoh547, | conact list:
Atom | Atom | Distance (A) | Mn | CB A:Asp194 | 4.50 | Mn | OD1 A:Asp194 | 4.43 | Mn | CG A:Asp194 | 4.96 | Mn | N A:Asp196 | 4.93 | Mn | CB A:Asp196 | 4.03 | Mn | OD2 A:Asp196 | 2.18 | Mn | OD1 A:Asp196 | 2.26 | Mn | CG A:Asp196 | 2.52 | Mn | CA A:Asp196 | 4.89 | Mn | OD1 A:Asn197 | 4.29 | Mn | CG A:Asn197 | 4.97 | Mn | NE2 A:His308 | 4.27 | Mn | CD2 A:His308 | 4.98 | Mn | CE1 A:His308 | 4.34 | Mn | O A:Thr309 | 4.35 | Mn | CD A:Arg310 | 4.92 | Mn | CG A:Arg310 | 4.19 | Mn | NH1 A:Arg310 | 4.39 | Mn | O3B A:Udp501 | 2.29 | Mn | PA A:Udp501 | 3.32 | Mn | O2A A:Udp501 | 2.27 | Mn | O1B A:Udp501 | 3.73 | Mn | PB A:Udp501 | 3.15 | Mn | C5' A:Udp501 | 4.86 | Mn | O5' A:Udp501 | 4.60 | Mn | O2B A:Udp501 | 4.46 | Mn | O3A A:Udp501 | 3.37 | Mn | O1A A:Udp501 | 4.14 | Mn | O A:Hoh504 | 2.25 | Mn | O A:Hoh505 | 2.32 | Mn | O A:Hoh522 | 4.79 | Mn | O A:Hoh547 | 4.08 |
| interactive model:
| Manganese binding site 2 out of 2 in 3cu0
|  Click to enlarge |  Click to enlarge | Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Manganese in the PDB 3cu0. 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: Asp194, B: Asp196, B: Asn197, B: His308, B: Thr309, B: Arg310, A: Udp503, A: Hoh514, B: Hoh505, B: Hoh506, B: Hoh542, | conact list:
Atom | Atom | Distance (A) | Mn | CB B:Asp194 | 4.59 | Mn | OD1 B:Asp194 | 4.51 | Mn | N B:Asp196 | 4.96 | Mn | CB B:Asp196 | 4.09 | Mn | OD2 B:Asp196 | 2.33 | Mn | OD1 B:Asp196 | 2.21 | Mn | CG B:Asp196 | 2.58 | Mn | CA B:Asp196 | 4.92 | Mn | OD1 B:Asn197 | 4.23 | Mn | CG B:Asn197 | 4.92 | Mn | NE2 B:His308 | 4.21 | Mn | ND1 B:His308 | 4.88 | Mn | CD2 B:His308 | 4.96 | Mn | CE1 B:His308 | 4.18 | Mn | O B:Thr309 | 4.33 | Mn | CD B:Arg310 | 4.93 | Mn | CG B:Arg310 | 4.20 | Mn | NH1 B:Arg310 | 3.98 | Mn | O3B A:Udp503 | 2.08 | Mn | PA A:Udp503 | 3.37 | Mn | O2A A:Udp503 | 2.33 | Mn | O1B A:Udp503 | 4.01 | Mn | PB A:Udp503 | 3.15 | Mn | C5' A:Udp503 | 4.86 | Mn | O5' A:Udp503 | 4.62 | Mn | O2B A:Udp503 | 4.33 | Mn | O3A A:Udp503 | 3.37 | Mn | O1A A:Udp503 | 4.20 | Mn | O A:Hoh514 | 4.02 | Mn | O B:Hoh505 | 2.24 | Mn | O B:Hoh506 | 2.28 | Mn | O B:Hoh542 | 4.79 |
| interactive model:
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