0.031646 0.000000 0.000000 0.000000 0.023753 0.000000 0.000000 0.000000 0.012255 0.00000 0.00000 0.00000 Benning, M.M. Meyer, T.E. Holden, H.M. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 4 90.00 90.00 90.00 31.600 42.100 81.600 C3 H7 N O2 89.093 y ALANINE L-peptide linking C6 H15 N4 O2 1 175.209 y ARGININE L-peptide linking C4 H8 N2 O3 132.118 y ASPARAGINE L-peptide linking C4 H7 N O4 133.103 y ASPARTIC ACID L-peptide linking C3 H7 N O2 S 121.158 y CYSTEINE L-peptide linking C5 H10 N2 O3 146.144 y GLUTAMINE L-peptide linking C5 H9 N O4 147.129 y GLUTAMIC ACID L-peptide linking C2 H5 N O2 75.067 y GLYCINE peptide linking C34 H34 Fe N4 O4 618.503 HEME C non-polymer C6 H10 N3 O2 1 156.162 y HISTIDINE L-peptide linking H2 O 18.015 WATER non-polymer C6 H13 N O2 131.173 y ISOLEUCINE L-peptide linking C6 H13 N O2 131.173 y LEUCINE L-peptide linking C6 H15 N2 O2 1 147.195 y LYSINE L-peptide linking C5 H11 N O2 S 149.211 y METHIONINE L-peptide linking C9 H11 N O2 165.189 y PHENYLALANINE L-peptide linking C5 H9 N O2 115.130 y PROLINE L-peptide linking C3 H7 N O3 105.093 y SERINE L-peptide linking C4 H9 N O3 119.119 y THREONINE L-peptide linking C11 H12 N2 O2 204.225 y TRYPTOPHAN L-peptide linking C9 H11 N O3 181.189 y TYROSINE L-peptide linking C5 H11 N O2 117.146 y VALINE L-peptide linking US Arch.Biochem.Biophys. ABBIA4 0158 0003-9861 310 460 466 10.1006/abbi.1994.1193 8179333 X-Ray structure of the cytochrome c2 isolated from Paracoccus denitrificans refined to 1.7-A resolution. 1994 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 1 x-ray 1 1.0 13842.557 CYTOCHROME C2 1 man polymer 618.503 HEME C 1 syn non-polymer 18.015 water 103 nat water no no QDGDAAKGEKEFNKCKACHMIQAPDGTDIIKGGKTGPNLYGVVGRKIASEEGFKYGEGILEVAEKNPDLTWTEADLIEYV TDPKPWLVKMTDDKGAKTKMTFKMGKNQADVVAFLAQNSPDAGGDGEAA QDGDAAKGEKEFNKCKACHMIQAPDGTDIIKGGKTGPNLYGVVGRKIASEEGFKYGEGILEVAEKNPDLTWTEADLIEYV TDPKPWLVKMTDDKGAKTKMTFKMGKNQADVVAFLAQNSPDAGGDGEAA A polypeptide(L) n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n Paracoccus sample 266 Paracoccus denitrificans 1.96 37.24 pdbx_database_status struct_conf struct_conf_type atom_site chem_comp entity pdbx_distant_solvent_atoms pdbx_entity_nonpoly pdbx_nonpoly_scheme pdbx_struct_conn_angle pdbx_validate_close_contact struct_conn struct_site repository Initial release Version format compliance Version format compliance Derived calculations Other Advisory Atomic model Data collection Derived calculations Non-polymer description Structure summary 1 0 1994-09-30 1 1 2008-03-24 1 2 2011-07-13 1 3 2017-11-29 2 0 2021-03-03 _pdbx_database_status.process_site _atom_site.B_iso_or_equiv _atom_site.Cartn_x _atom_site.Cartn_y _atom_site.Cartn_z _atom_site.auth_atom_id _atom_site.auth_comp_id _atom_site.label_atom_id _atom_site.label_comp_id _atom_site.type_symbol _chem_comp.formula _chem_comp.formula_weight _chem_comp.id _chem_comp.name _chem_comp.pdbx_synonyms _entity.formula_weight _entity.pdbx_description _pdbx_entity_nonpoly.comp_id _pdbx_entity_nonpoly.name _pdbx_nonpoly_scheme.mon_id _pdbx_nonpoly_scheme.pdb_mon_id _pdbx_struct_conn_angle.ptnr1_auth_comp_id _pdbx_struct_conn_angle.ptnr1_label_comp_id _pdbx_struct_conn_angle.ptnr2_auth_comp_id _pdbx_struct_conn_angle.ptnr2_label_comp_id _pdbx_struct_conn_angle.ptnr3_auth_comp_id _pdbx_struct_conn_angle.ptnr3_label_comp_id _pdbx_validate_close_contact.auth_comp_id_2 _struct_conn.pdbx_leaving_atom_flag _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_atom_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_atom_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_site.details _struct_site.pdbx_auth_asym_id _struct_site.pdbx_auth_comp_id _struct_site.pdbx_auth_seq_id Y BNL 1994-07-06 REL 1 A O HOH 157 6.45 1 A O HOH 158 6.79 1 A O HOH 202 6.12 HEC HEME C HOH water HEM 125 2 HEC HEC 130 A HOH 1 3 HOH HOH 131 A HOH 2 3 HOH HOH 132 A HOH 3 3 HOH HOH 133 A HOH 4 3 HOH HOH 134 A HOH 5 3 HOH HOH 135 A HOH 6 3 HOH HOH 136 A HOH 7 3 HOH HOH 137 A HOH 8 3 HOH HOH 138 A HOH 9 3 HOH HOH 139 A HOH 10 3 HOH HOH 140 A HOH 11 3 HOH HOH 141 A HOH 12 3 HOH HOH 142 A HOH 13 3 HOH HOH 143 A HOH 14 3 HOH HOH 144 A HOH 15 3 HOH HOH 145 A HOH 16 3 HOH HOH 146 A HOH 17 3 HOH HOH 147 A HOH 18 3 HOH HOH 148 A HOH 19 3 HOH HOH 149 A HOH 20 3 HOH HOH 150 A HOH 21 3 HOH HOH 151 A HOH 22 3 HOH HOH 152 A HOH 23 3 HOH HOH 153 A HOH 24 3 HOH HOH 154 A HOH 25 3 HOH HOH 155 A HOH 26 3 HOH HOH 156 A HOH 27 3 HOH HOH 157 A HOH 28 3 HOH HOH 158 A HOH 29 3 HOH HOH 159 A HOH 30 3 HOH HOH 160 A HOH 31 3 HOH HOH 161 A HOH 32 3 HOH HOH 162 A HOH 33 3 HOH HOH 163 A HOH 34 3 HOH HOH 164 A HOH 35 3 HOH HOH 165 A HOH 36 3 HOH HOH 166 A HOH 37 3 HOH HOH 167 A HOH 38 3 HOH HOH 168 A HOH 39 3 HOH HOH 169 A HOH 40 3 HOH HOH 170 A HOH 41 3 HOH HOH 171 A HOH 42 3 HOH HOH 172 A HOH 43 3 HOH HOH 173 A HOH 44 3 HOH HOH 174 A HOH 45 3 HOH HOH 175 A HOH 46 3 HOH HOH 176 A HOH 47 3 HOH HOH 177 A HOH 48 3 HOH HOH 178 A HOH 49 3 HOH HOH 179 A HOH 50 3 HOH HOH 180 A HOH 51 3 HOH HOH 181 A HOH 52 3 HOH HOH 182 A HOH 53 3 HOH HOH 183 A HOH 54 3 HOH HOH 184 A HOH 55 3 HOH HOH 185 A HOH 56 3 HOH HOH 186 A HOH 57 3 HOH HOH 187 A HOH 58 3 HOH HOH 188 A HOH 59 3 HOH HOH 189 A HOH 60 3 HOH HOH 190 A HOH 61 3 HOH HOH 191 A HOH 62 3 HOH HOH 192 A HOH 63 3 HOH HOH 193 A HOH 64 3 HOH HOH 194 A HOH 65 3 HOH HOH 195 A HOH 66 3 HOH HOH 196 A HOH 67 3 HOH HOH 197 A HOH 68 3 HOH HOH 198 A HOH 69 3 HOH HOH 199 A HOH 70 3 HOH HOH 200 A HOH 71 3 HOH HOH 201 A HOH 72 3 HOH HOH 202 A HOH 73 3 HOH HOH 203 A HOH 74 3 HOH HOH 204 A HOH 75 3 HOH HOH 205 A HOH 76 3 HOH HOH 206 A HOH 77 3 HOH HOH 207 A HOH 78 3 HOH HOH 208 A HOH 79 3 HOH HOH 209 A HOH 80 3 HOH HOH 210 A HOH 81 3 HOH HOH 211 A HOH 82 3 HOH HOH 212 A HOH 83 3 HOH HOH 213 A HOH 84 3 HOH HOH 214 A HOH 85 3 HOH HOH 215 A HOH 86 3 HOH HOH 216 A HOH 87 3 HOH HOH 217 A HOH 88 3 HOH HOH 218 A HOH 89 3 HOH HOH 219 A HOH 90 3 HOH HOH 220 A HOH 91 3 HOH HOH 221 A HOH 92 3 HOH HOH 222 A HOH 93 3 HOH HOH 223 A HOH 94 3 HOH HOH 224 A HOH 95 3 HOH HOH 225 A HOH 96 3 HOH HOH 226 A HOH 97 3 HOH HOH 227 A HOH 98 3 HOH HOH 228 A HOH 99 3 HOH HOH 229 A HOH 100 3 HOH HOH 230 A HOH 101 3 HOH HOH 231 A HOH 102 3 HOH HOH 232 A HOH 103 3 HOH HOH 233 A n 1 1 A ASP 2 n 2 ASP 2 A GLY 3 n 3 GLY 3 A ASP 4 n 4 ASP 4 A ALA 5 n 5 ALA 5 A ALA 6 n 6 ALA 6 A LYS 7 n 7 LYS 7 A GLY 8 n 8 GLY 8 A GLU 9 n 9 GLU 9 A LYS 10 n 10 LYS 10 A GLU 11 n 11 GLU 11 A PHE 12 n 12 PHE 12 A ASN 13 n 13 ASN 13 A LYS 14 n 14 LYS 14 A CYS 15 n 15 CYS 15 A LYS 16 n 16 LYS 16 A ALA 17 n 17 ALA 17 A CYS 18 n 18 CYS 18 A HIS 19 n 19 HIS 19 A MET 20 n 20 MET 20 A ILE 21 n 21 ILE 21 A GLN 22 n 22 GLN 22 A ALA 23 n 23 ALA 23 A PRO 24 n 24 PRO 24 A ASP 25 n 25 ASP 25 A GLY 26 n 26 GLY 26 A THR 27 n 27 THR 27 A ASP 28 n 28 ASP 28 A ILE 29 n 29 ILE 29 A ILE 30 n 30 ILE 30 A LYS 31 n 31 LYS 31 A GLY 32 n 32 GLY 32 A GLY 33 n 33 GLY 33 A LYS 34 n 34 LYS 34 A THR 35 n 35 THR 35 A GLY 36 n 36 GLY 36 A PRO 37 n 37 PRO 37 A ASN 38 n 38 ASN 38 A LEU 39 n 39 LEU 39 A TYR 40 n 40 TYR 40 A GLY 41 n 41 GLY 41 A VAL 42 n 42 VAL 42 A VAL 43 n 43 VAL 43 A GLY 44 n 44 GLY 44 A ARG 45 n 45 ARG 45 A LYS 46 n 46 LYS 46 A ILE 47 n 47 ILE 47 A ALA 48 n 48 ALA 48 A SER 49 n 49 SER 49 A GLU 50 n 50 GLU 50 A GLU 51 n 51 GLU 51 A GLY 52 n 52 GLY 52 A PHE 53 n 53 PHE 53 A LYS 54 n 54 LYS 54 A TYR 55 n 55 TYR 55 A GLY 56 n 56 GLY 56 A GLU 57 n 57 GLU 57 A GLY 58 n 58 GLY 58 A ILE 59 n 59 ILE 59 A LEU 60 n 60 LEU 60 A GLU 61 n 61 GLU 61 A VAL 62 n 62 VAL 62 A ALA 63 n 63 ALA 63 A GLU 64 n 64 GLU 64 A LYS 65 n 65 LYS 65 A ASN 66 n 66 ASN 66 A PRO 67 n 67 PRO 67 A ASP 68 n 68 ASP 68 A LEU 69 n 69 LEU 69 A THR 70 n 70 THR 70 A TRP 71 n 71 TRP 71 A THR 72 n 72 THR 72 A GLU 73 n 73 GLU 73 A ALA 74 n 74 ALA 74 A ASP 75 n 75 ASP 75 A LEU 76 n 76 LEU 76 A ILE 77 n 77 ILE 77 A GLU 78 n 78 GLU 78 A TYR 79 n 79 TYR 79 A VAL 80 n 80 VAL 80 A THR 81 n 81 THR 81 A ASP 82 n 82 ASP 82 A PRO 83 n 83 PRO 83 A LYS 84 n 84 LYS 84 A PRO 85 n 85 PRO 85 A TRP 86 n 86 TRP 86 A LEU 87 n 87 LEU 87 A VAL 88 n 88 VAL 88 A LYS 89 n 89 LYS 89 A MET 90 n 90 MET 90 A THR 91 n 91 THR 91 A ASP 92 n 92 ASP 92 A ASP 93 n 93 ASP 93 A LYS 94 n 94 LYS 94 A GLY 95 n 95 GLY 95 A ALA 96 n 96 ALA 96 A LYS 97 n 97 LYS 97 A THR 98 n 98 THR 98 A LYS 99 n 99 LYS 99 A MET 100 n 100 MET 100 A THR 101 n 101 THR 101 A PHE 102 n 102 PHE 102 A LYS 103 n 103 LYS 103 A MET 104 n 104 MET 104 A GLY 105 n 105 GLY 105 A LYS 106 n 106 LYS 106 A ASN 107 n 107 ASN 107 A GLN 108 n 108 GLN 108 A ALA 109 n 109 ALA 109 A ASP 110 n 110 ASP 110 A VAL 111 n 111 VAL 111 A VAL 112 n 112 VAL 112 A ALA 113 n 113 ALA 113 A PHE 114 n 114 PHE 114 A LEU 115 n 115 LEU 115 A ALA 116 n 116 ALA 116 A GLN 117 n 117 GLN 117 A ASN 118 n 118 ASN 118 A SER 119 n 119 SER 119 A PRO 120 n 120 PRO 120 A ASP 121 n 121 ASP 121 A ALA 122 n 122 ALA 122 A n 123 123 A n 124 124 A n 125 125 A n 126 126 A n 127 127 A n 128 128 A n 129 129 A author_defined_assembly 1 monomeric A HIS 19 A NE2 HIS 19 1_555 A HEC 130 B FE HEC 1_555 A HEC 130 B NA HEC 1_555 91.7 A HIS 19 A NE2 HIS 19 1_555 A HEC 130 B FE HEC 1_555 A HEC 130 B NB HEC 1_555 90.2 A HEC 130 B NA HEC 1_555 A HEC 130 B FE HEC 1_555 A HEC 130 B NB HEC 1_555 90.4 A HIS 19 A NE2 HIS 19 1_555 A HEC 130 B FE HEC 1_555 A HEC 130 B NC HEC 1_555 87.9 A HEC 130 B NA HEC 1_555 A HEC 130 B FE HEC 1_555 A HEC 130 B NC HEC 1_555 177.9 A HEC 130 B NB HEC 1_555 A HEC 130 B FE HEC 1_555 A HEC 130 B NC HEC 1_555 87.5 A HIS 19 A NE2 HIS 19 1_555 A HEC 130 B FE HEC 1_555 A HEC 130 B ND HEC 1_555 89.9 A HEC 130 B NA HEC 1_555 A HEC 130 B FE HEC 1_555 A HEC 130 B ND HEC 1_555 91.5 A HEC 130 B NB HEC 1_555 A HEC 130 B FE HEC 1_555 A HEC 130 B ND HEC 1_555 178.1 A HEC 130 B NC HEC 1_555 A HEC 130 B FE HEC 1_555 A HEC 130 B ND HEC 1_555 90.5 A HIS 19 A NE2 HIS 19 1_555 A HEC 130 B FE HEC 1_555 A MET 100 A SD MET 100 1_555 173.5 A HEC 130 B NA HEC 1_555 A HEC 130 B FE HEC 1_555 A MET 100 A SD MET 100 1_555 83.4 A HEC 130 B NB HEC 1_555 A HEC 130 B FE HEC 1_555 A MET 100 A SD MET 100 1_555 94.0 A HEC 130 B NC HEC 1_555 A HEC 130 B FE HEC 1_555 A MET 100 A SD MET 100 1_555 97.2 A HEC 130 B ND HEC 1_555 A HEC 130 B FE HEC 1_555 A MET 100 A SD MET 100 1_555 86.1 1.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 1_555 x,y,z identity operation 0.0000000000 0.0000000000 0.0000000000 1 A CB ASP 2 A CB ASP 2 1 Y 1 A CG ASP 2 A CG ASP 2 1 Y 1 A OD1 ASP 2 A OD1 ASP 2 1 Y 1 A OD2 ASP 2 A OD2 ASP 2 1 Y 1 A GLN 1 A GLN 1 1 Y 1 A GLY 123 A GLY 123 1 Y 1 A GLY 124 A GLY 124 1 Y 1 A ASP 125 A ASP 125 1 Y 1 A GLY 126 A GLY 126 1 Y 1 A GLU 127 A GLU 127 1 Y 1 A ALA 128 A ALA 128 1 Y 1 A ALA 129 A ALA 129 1 Y 1 A A SG CAC CYS HEC 18 130 2.11 1 -5.78 0.90 118.30 112.52 A A A CB CG OD1 ASP ASP ASP 25 25 25 N 1 5.60 0.90 118.30 123.90 A A A CB CG OD2 ASP ASP ASP 25 25 25 N 1 6.28 0.90 118.30 124.58 A A A CB CG OD1 ASP ASP ASP 68 68 68 N 1 -6.28 0.90 118.30 112.02 A A A CB CG OD2 ASP ASP ASP 68 68 68 N 1 -5.54 0.90 118.30 112.76 A A A CB CG OD1 ASP ASP ASP 75 75 75 N 1 -5.96 0.90 118.30 112.34 A A A CB CG OD2 ASP ASP ASP 92 92 92 N 1 A ASP 82 -176.94 102.31 0.1750000 1.7 30.0 12199 1 1.7 30.0 103 1063 43 0 917 0.007 2.26 refinement TNT CYTOCHROME C2 (FORMERLY CYTOCHROME C550) X-RAY STRUCTURE OF THE CYTOCHROME C2 ISOLATED FROM PARACOCCUS DENITRIFICANS REFINED TO 1.7 ANGSTROMS RESOLUTION 1 N N 2 N N 3 N N A ALA 5 A ALA 5 HELX_P A CYS 15 A CYS 15 1 H1 11 A GLU 57 A GLU 57 HELX_P A LYS 65 A LYS 65 1 H2 9 A GLU 73 A GLU 73 HELX_P A THR 81 A THR 81 1 H3 9 A PRO 83 A PRO 83 HELX_P A THR 91 A THR 91 1 H4 9 A GLN 108 A GLN 108 HELX_P A GLN 117 A GLN 117 1 H5 10 covale 1.841 none A CYS 15 A SG CYS 15 1_555 A HEC 130 B CAB HEC 1_555 metalc 1.927 A HIS 19 A NE2 HIS 19 1_555 A HEC 130 B FE HEC 1_555 metalc 2.358 A MET 100 A SD MET 100 1_555 A HEC 130 B FE HEC 1_555 ELECTRON TRANSPORT ELECTRON TRANSPORT CY550_PARDE UNP 1 1 P00096 MKISIYATLAAITLALPAAAQDGDAAKGEKEFNKCKACHMIQAPDGTDIIKGGKTGPNLYGVVGRKIASEEGFKYGEGIL EVAEKNPDLTWTEADLIEYVTDPKPWLVKMTDDKGAKTKMTFKMGKNQADVVAFLAQNSPDAGGDGEAAAEGESN 21 149 1COT 1 129 P00096 A 1 1 129 2 parallel A MET 20 A MET 20 A GLN 22 A GLN 22 A THR 27 A THR 27 A ILE 30 A ILE 30 BINDING SITE FOR RESIDUE HEC A 130 A HEC 130 Software 22 A LYS 14 A LYS 14 22 1_555 A CYS 15 A CYS 15 22 1_555 A CYS 18 A CYS 18 22 1_555 A HIS 19 A HIS 19 22 1_555 A THR 35 A THR 35 22 1_555 A PRO 37 A PRO 37 22 1_555 A ARG 45 A ARG 45 22 1_555 A ALA 48 A ALA 48 22 1_555 A PHE 53 A PHE 53 22 1_555 A TYR 55 A TYR 55 22 1_555 A GLY 56 A GLY 56 22 1_555 A ILE 59 A ILE 59 22 1_555 A TRP 71 A TRP 71 22 1_555 A LEU 76 A LEU 76 22 1_555 A TYR 79 A TYR 79 22 1_555 A VAL 80 A VAL 80 22 1_555 A PRO 85 A PRO 85 22 4_456 A LYS 99 A LYS 99 22 1_555 A MET 100 A MET 100 22 1_555 A HOH 135 C HOH 22 1_555 A HOH 136 C HOH 22 1_555 A HOH 145 C HOH 22 1_555 19 P 21 21 21