0.011641 0.006721 0.000000 0.000000 0.013442 0.000000 0.000000 0.000000 0.010204 0.00000 0.00000 0.00000 Cioni, P. Pesce, A. Rocca, B.M.D. Castelli, S. Falconi, M. Parrilli, L. Bolognesi, M. Strambini, G. Desideri, A. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 18 90.00 90.00 120.00 85.900 85.900 98.000 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 Cu 2 63.546 COPPER (II) ION non-polymer 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 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 Zn 2 65.409 ZINC ION non-polymer UK J.Mol.Biol. JMOBAK 0070 0022-2836 326 1351 10.1016/S0022-2836(03)00047-0 12595249 Active-Site Copper and Zinc Ions Modulate the Quaternary Structure of Prokaryotic Cu,Zn Superoxide Dismutase 2003 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 100.0 1 CCD 2001-04-28 MARRESEARCH SINGLE WAVELENGTH M x-ray 1 1.0 1.0 ID14-3 ESRF 1.0 SYNCHROTRON ESRF BEAMLINE ID14-3 15799.761 SUPEROXIDE DISMUTASE 1.15.1.1 YES 1 man polymer 65.409 ZINC ION 1 syn non-polymer 63.546 COPPER (II) ION 1 syn non-polymer 18.015 water 91 nat water no no QDLTVKMTDLQTGKPVGTIELSQNDYGVVFIPELADLTPGMHGFHIHQNGSCASSEKDGKVVLGGAAGGHYDPEHTNKHG FPWTDDNHKGDLPALFVSANGLATNPVLAPRLTLKELKGHAIMIHAGGDNHSDMPKALGGGGARVACGVIQ QDLTVKMTDLQTGKPVGTIELSQNDYGVVFIPELADLTPGMHGFHIHQNGSCASSEKDGKVVLGGAAGGHYDPEHTNKHG FPWTDDNHKGDLPALFVSANGLATNPVLAPRLTLKELKGHAIMIHAGGDNHSDMPKALGGGGARVACGVIQ 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 n n n n n n n n n n n n n n n n n n n n n n sample 658 PHOTOBACTERIUM LEIOGNATHI 562 ESCHERICHIA COLI 71/18 PEMBL18 1 3.40 64 VAPOR DIFFUSION, SITTING DROP 4.00 PEG 8,000 25%, NACL 100 MM, SODIUM ACETATE 50 MM, PH 4, TEMPERATURE 28C 301 atom_site exptl_crystal_grow pdbx_database_proc pdbx_database_status pdbx_unobs_or_zero_occ_atoms pdbx_unobs_or_zero_occ_residues struct_biol repository Initial release Version format compliance Version format compliance Advisory Atomic model Data collection Experimental preparation Other 1 0 2003-02-27 1 1 2011-05-08 1 2 2011-07-13 2 0 2019-03-13 _atom_site.occupancy _exptl_crystal_grow.method _exptl_crystal_grow.temp _pdbx_database_status.recvd_author_approval THREE-DIMENSIONAL STRUCTURE OF PROKARYOTIC CU, ZN SUPEROXIDE DISMUTASE FROM P.LEIOGNATHI, SOLVED BY X-RAY CRYSTALLOGRAPHY. X-RAY 3D STRUCTURE OF P.LEIOGNATHI CU,ZN SOD MUTANT W83Y X-RAY 3D STRUCTURE OF P.LEIOGNATHI CU,ZN SOD MUTANT W83F X-RAY 3D STRUCTURE OF P.LEIOGNATHI CU,ZN SOD MUTANT V29A X-RAY 3D STRUCTURE OF P.LEIOGNATHI CU,ZN SOD MUTANT V29G X-RAY 3D STRUCTURE OF P.LEIOGNATHI CU,ZN SOD MUTANT M41I X-RAY STRUCTURE OF A BACTERIAL COPPER,ZINC SUPEROXIDE DISMUTASE ACTIVE SITE COPPER AND ZINC IONS MODULATE THE QUATERNARY STRUCTURE OF PROKARYOTIC CU, ZN SUPEROXIDE DISMUTASE PDBE Y PDBE 2003-01-14 REL ZN ZINC ION CU COPPER (II) ION HOH water MUTATED RESIDUES: LYS 25 ASP THE PROTEIN USED IS A TRUNCATED FORM, WITHOUT THE FIRST 22 RESIDUES SIGNAL SEQUENCE ZN 1152 2 ZN ZN 1152 A CU 1153 3 CU CU 1153 A HOH 2001 4 HOH HOH 2001 A HOH 2002 4 HOH HOH 2002 A HOH 2003 4 HOH HOH 2003 A HOH 2004 4 HOH HOH 2004 A HOH 2005 4 HOH HOH 2005 A HOH 2006 4 HOH HOH 2006 A HOH 2007 4 HOH HOH 2007 A HOH 2008 4 HOH HOH 2008 A HOH 2009 4 HOH HOH 2009 A HOH 2010 4 HOH HOH 2010 A HOH 2011 4 HOH HOH 2011 A HOH 2012 4 HOH HOH 2012 A HOH 2013 4 HOH HOH 2013 A HOH 2014 4 HOH HOH 2014 A HOH 2015 4 HOH HOH 2015 A HOH 2016 4 HOH HOH 2016 A HOH 2017 4 HOH HOH 2017 A HOH 2018 4 HOH HOH 2018 A HOH 2019 4 HOH HOH 2019 A HOH 2020 4 HOH HOH 2020 A HOH 2021 4 HOH HOH 2021 A HOH 2022 4 HOH HOH 2022 A HOH 2023 4 HOH HOH 2023 A HOH 2024 4 HOH HOH 2024 A HOH 2025 4 HOH HOH 2025 A HOH 2026 4 HOH HOH 2026 A HOH 2027 4 HOH HOH 2027 A HOH 2028 4 HOH HOH 2028 A HOH 2029 4 HOH HOH 2029 A HOH 2030 4 HOH HOH 2030 A HOH 2031 4 HOH HOH 2031 A HOH 2032 4 HOH HOH 2032 A HOH 2033 4 HOH HOH 2033 A HOH 2034 4 HOH HOH 2034 A HOH 2035 4 HOH HOH 2035 A HOH 2036 4 HOH HOH 2036 A HOH 2037 4 HOH HOH 2037 A HOH 2038 4 HOH HOH 2038 A HOH 2039 4 HOH HOH 2039 A HOH 2040 4 HOH HOH 2040 A HOH 2041 4 HOH HOH 2041 A HOH 2042 4 HOH HOH 2042 A HOH 2043 4 HOH HOH 2043 A HOH 2044 4 HOH HOH 2044 A HOH 2045 4 HOH HOH 2045 A HOH 2046 4 HOH HOH 2046 A HOH 2047 4 HOH HOH 2047 A HOH 2048 4 HOH HOH 2048 A HOH 2049 4 HOH HOH 2049 A HOH 2050 4 HOH HOH 2050 A HOH 2051 4 HOH HOH 2051 A HOH 2052 4 HOH HOH 2052 A HOH 2053 4 HOH HOH 2053 A HOH 2054 4 HOH HOH 2054 A HOH 2055 4 HOH HOH 2055 A HOH 2056 4 HOH HOH 2056 A HOH 2057 4 HOH HOH 2057 A HOH 2058 4 HOH HOH 2058 A HOH 2059 4 HOH HOH 2059 A HOH 2060 4 HOH HOH 2060 A HOH 2061 4 HOH HOH 2061 A HOH 2062 4 HOH HOH 2062 A HOH 2063 4 HOH HOH 2063 A HOH 2064 4 HOH HOH 2064 A HOH 2065 4 HOH HOH 2065 A HOH 2066 4 HOH HOH 2066 A HOH 2067 4 HOH HOH 2067 A HOH 2068 4 HOH HOH 2068 A HOH 2069 4 HOH HOH 2069 A HOH 2070 4 HOH HOH 2070 A HOH 2071 4 HOH HOH 2071 A HOH 2072 4 HOH HOH 2072 A HOH 2073 4 HOH HOH 2073 A HOH 2074 4 HOH HOH 2074 A HOH 2075 4 HOH HOH 2075 A HOH 2076 4 HOH HOH 2076 A HOH 2077 4 HOH HOH 2077 A HOH 2078 4 HOH HOH 2078 A HOH 2079 4 HOH HOH 2079 A HOH 2080 4 HOH HOH 2080 A HOH 2081 4 HOH HOH 2081 A HOH 2082 4 HOH HOH 2082 A HOH 2083 4 HOH HOH 2083 A HOH 2084 4 HOH HOH 2084 A HOH 2085 4 HOH HOH 2085 A HOH 2086 4 HOH HOH 2086 A HOH 2087 4 HOH HOH 2087 A HOH 2088 4 HOH HOH 2088 A HOH 2089 4 HOH HOH 2089 A HOH 2090 4 HOH HOH 2090 A HOH 2091 4 HOH HOH 2091 A GLN 1 n 1 GLN 1 A ASP 2 n 2 ASP 2 A LEU 3 n 3 LEU 3 A THR 4 n 4 THR 4 A VAL 5 n 5 VAL 5 A LYS 6 n 6 LYS 6 A MET 7 n 7 MET 7 A THR 8 n 8 THR 8 A ASP 9 n 9 ASP 9 A LEU 10 n 10 LEU 10 A GLN 11 n 11 GLN 11 A THR 12 n 12 THR 12 A GLY 13 n 13 GLY 13 A LYS 14 n 14 LYS 14 A PRO 15 n 15 PRO 15 A VAL 16 n 16 VAL 16 A GLY 17 n 17 GLY 17 A THR 18 n 18 THR 18 A ILE 19 n 19 ILE 19 A GLU 20 n 20 GLU 20 A LEU 21 n 21 LEU 21 A SER 22 n 22 SER 22 A GLN 23 n 23 GLN 23 A ASN 24 n 24 ASN 24 A ASP 25 n 25 ASP 25 A TYR 26 n 26 TYR 26 A GLY 27 n 27 GLY 27 A VAL 28 n 28 VAL 28 A VAL 29 n 29 VAL 29 A PHE 30 n 30 PHE 30 A ILE 31 n 31 ILE 31 A PRO 32 n 32 PRO 32 A GLU 33 n 33 GLU 33 A LEU 34 n 34 LEU 34 A ALA 35 n 35 ALA 35 A ASP 36 n 36 ASP 36 A LEU 37 n 37 LEU 37 A THR 38 n 38 THR 38 A PRO 39 n 39 PRO 39 A GLY 40 n 40 GLY 40 A MET 41 n 41 MET 41 A HIS 42 n 42 HIS 42 A GLY 43 n 43 GLY 43 A PHE 44 n 44 PHE 44 A HIS 45 n 45 HIS 45 A ILE 46 n 46 ILE 46 A HIS 47 n 47 HIS 47 A GLN 48 n 48 GLN 48 A ASN 49 n 49 ASN 49 A GLY 50 n 50 GLY 50 A SER 51 n 51 SER 51 A CYS 52 n 52 CYS 52 A ALA 53 n 53 ALA 53 A SER 54 n 54 SER 54 A SER 55 n 55 SER 55 A GLU 56 n 56 GLU 56 A LYS 57 n 57 LYS 57 A ASP 58 n 58 ASP 58 A GLY 59 n 59 GLY 59 A LYS 60 n 60 LYS 60 A VAL 61 n 61 VAL 61 A VAL 62 n 62 VAL 62 A LEU 63 n 63 LEU 63 A GLY 64 n 64 GLY 64 A GLY 65 n 65 GLY 65 A ALA 66 n 66 ALA 66 A ALA 67 n 67 ALA 67 A GLY 68 n 68 GLY 68 A GLY 69 n 69 GLY 69 A HIS 70 n 70 HIS 70 A TYR 71 n 71 TYR 71 A ASP 72 n 72 ASP 72 A PRO 73 n 73 PRO 73 A GLU 74 n 74 GLU 74 A HIS 75 n 75 HIS 75 A THR 76 n 76 THR 76 A ASN 77 n 77 ASN 77 A LYS 78 n 78 LYS 78 A HIS 79 n 79 HIS 79 A GLY 80 n 80 GLY 80 A PHE 81 n 81 PHE 81 A PRO 82 n 82 PRO 82 A TRP 83 n 83 TRP 83 A THR 84 n 84 THR 84 A ASP 85 n 85 ASP 85 A ASP 86 n 86 ASP 86 A ASN 87 n 87 ASN 87 A HIS 88 n 88 HIS 88 A LYS 89 n 89 LYS 89 A GLY 90 n 90 GLY 90 A ASP 91 n 91 ASP 91 A LEU 92 n 92 LEU 92 A PRO 93 n 93 PRO 93 A ALA 94 n 94 ALA 94 A LEU 95 n 95 LEU 95 A PHE 96 n 96 PHE 96 A VAL 97 n 97 VAL 97 A SER 98 n 98 SER 98 A ALA 99 n 99 ALA 99 A ASN 100 n 100 ASN 100 A GLY 101 n 101 GLY 101 A LEU 102 n 102 LEU 102 A ALA 103 n 103 ALA 103 A THR 104 n 104 THR 104 A ASN 105 n 105 ASN 105 A PRO 106 n 106 PRO 106 A VAL 107 n 107 VAL 107 A LEU 108 n 108 LEU 108 A ALA 109 n 109 ALA 109 A PRO 110 n 110 PRO 110 A ARG 111 n 111 ARG 111 A LEU 112 n 112 LEU 112 A THR 113 n 113 THR 113 A LEU 114 n 114 LEU 114 A LYS 115 n 115 LYS 115 A GLU 116 n 116 GLU 116 A LEU 117 n 117 LEU 117 A LYS 118 n 118 LYS 118 A GLY 119 n 119 GLY 119 A HIS 120 n 120 HIS 120 A ALA 121 n 121 ALA 121 A ILE 122 n 122 ILE 122 A MET 123 n 123 MET 123 A ILE 124 n 124 ILE 124 A HIS 125 n 125 HIS 125 A ALA 126 n 126 ALA 126 A GLY 127 n 127 GLY 127 A GLY 128 n 128 GLY 128 A ASP 129 n 129 ASP 129 A ASN 130 n 130 ASN 130 A HIS 131 n 131 HIS 131 A SER 132 n 132 SER 132 A ASP 133 n 133 ASP 133 A MET 134 n 134 MET 134 A PRO 135 n 135 PRO 135 A LYS 136 n 136 LYS 136 A ALA 137 n 137 ALA 137 A LEU 138 n 138 LEU 138 A GLY 139 n 139 GLY 139 A GLY 140 n 140 GLY 140 A GLY 141 n 141 GLY 141 A GLY 142 n 142 GLY 142 A ALA 143 n 143 ALA 143 A ARG 144 n 144 ARG 144 A VAL 145 n 145 VAL 145 A ALA 146 n 146 ALA 146 A CYS 147 n 147 CYS 147 A GLY 148 n 148 GLY 148 A VAL 149 n 149 VAL 149 A ILE 150 n 150 ILE 150 A GLN 151 n 151 GLN 151 A author_and_software_defined_assembly PQS 2 dimeric A HIS 88 A ND1 HIS 88 1_555 A ZN 1152 B ZN ZN 1_555 A ASP 91 A OD1 ASP 91 1_555 117.9 A HIS 88 A ND1 HIS 88 1_555 A ZN 1152 B ZN ZN 1_555 A HIS 70 A ND1 HIS 70 1_555 102.6 A ASP 91 A OD1 ASP 91 1_555 A ZN 1152 B ZN ZN 1_555 A HIS 70 A ND1 HIS 70 1_555 107.8 A HIS 88 A ND1 HIS 88 1_555 A ZN 1152 B ZN ZN 1_555 A HIS 79 A ND1 HIS 79 1_555 124.5 A ASP 91 A OD1 ASP 91 1_555 A ZN 1152 B ZN ZN 1_555 A HIS 79 A ND1 HIS 79 1_555 97.1 A HIS 70 A ND1 HIS 70 1_555 A ZN 1152 B ZN ZN 1_555 A HIS 79 A ND1 HIS 79 1_555 106.0 A HIS 45 A ND1 HIS 45 1_555 A CU 1153 C CU CU 1_555 A HIS 125 A NE2 HIS 125 1_555 102.5 A HIS 45 A ND1 HIS 45 1_555 A CU 1153 C CU CU 1_555 A HIS 47 A NE2 HIS 47 1_555 142.5 A HIS 125 A NE2 HIS 125 1_555 A CU 1153 C CU CU 1_555 A HIS 47 A NE2 HIS 47 1_555 113.3 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 1.0000000000 0.0000000000 0.0000000000 0.0000000000 -1.0000000000 0.0000000000 0.0000000000 0.0000000000 -1.0000000000 11_565 x-y+2/3,-y+4/3,-z+1/3 crystal symmetry operation 0.0000000000 99.1887762468 32.6666666667 A N HIS 47 A N HIS 47 A O ALA 121 A O ALA 121 A O ILE 124 A O ILE 124 A N VAL 145 A N VAL 145 A N CYS 147 A N CYS 147 A O THR 8 A O THR 8 A O MET 7 A O MET 7 A N VAL 16 A N VAL 16 A N ASN 24 A N ASN 24 A O GLY 27 A O GLY 27 A N PHE 30 A N PHE 30 A O VAL 107 A O VAL 107 A N HIS 42 A N HIS 42 A O LEU 95 A O LEU 95 A N LYS 57 A N LYS 57 A O LYS 60 A O LYS 60 1 A HOH 2021 D HOH 1 A A O O HOH HOH 2003 2004 0.78 1 A A O O HOH HOH 2077 2077 0.42 1_555 4_555 1 A ASP 72 -155.19 63.11 1 A ASP 86 -91.20 55.27 1 A ALA 143 -48.63 151.44 19 0.231 0.183 0.191 1.73 30.0 1499 14997 10.0 97.5 0.085 RANDOM 1 0.000 OTHER 0.13 0.131 1.73 30.0 91 1201 2 0 1108 18 1.730 30.000 1OAJ 14997 0.03700 1 20.0000 2.500 97.5 0.17800 1.73 1.76 5.000 1 75.8 refinement REFMAC data reduction DENZO data scaling SCALEPACK phasing CCP4 SUPEROXIDE DISMUTASE (E.C.1.15.1.1) Active site copper and zinc ions modulate the quaternary structure of prokaryotic Cu,Zn superoxide dismutase 1 N N 2 N N 3 N N 4 N N A GLY 64 A GLY 64 HELX_P A GLY 68 A GLY 68 5 1 5 A THR 113 A THR 113 HELX_P A LYS 118 A LYS 118 1 2 6 A LYS 136 A LYS 136 HELX_P A GLY 141 A GLY 141 5 3 6 disulf 2.184 A CYS 52 A SG CYS 52 1_555 A CYS 147 A SG CYS 147 1_555 metalc 1.993 A ZN 1152 B ZN ZN 1_555 A HIS 88 A ND1 HIS 88 1_555 metalc 1.924 A ZN 1152 B ZN ZN 1_555 A ASP 91 A OD1 ASP 91 1_555 metalc 1.957 A ZN 1152 B ZN ZN 1_555 A HIS 70 A ND1 HIS 70 1_555 metalc 2.084 A ZN 1152 B ZN ZN 1_555 A HIS 79 A ND1 HIS 79 1_555 metalc 2.046 A CU 1153 C CU CU 1_555 A HIS 45 A ND1 HIS 45 1_555 metalc 2.070 A CU 1153 C CU CU 1_555 A HIS 125 A NE2 HIS 125 1_555 metalc 1.933 A CU 1153 C CU CU 1_555 A HIS 47 A NE2 HIS 47 1_555 OXIDOREDUCTASE OXIDOREDUCTASE, PROKARIOTIC CU, ZN SUPEROXIDE DISMUTASE, SUBUNIT INTERACTION RECOGNITION, PROTEIN ELECTROSTATIC A MET 134 A MET 134 1 A PRO 135 A PRO 135 0.45 SODC_PHOLE UNP 1 P00446 23 173 1OAJ 1 151 P00446 A 1 1 151 1 LYS engineered mutation ASP 25 1OAJ A P00446 UNP 47 25 1 THR conflict ILE 31 1OAJ A P00446 UNP 53 31 7 2 2 anti-parallel anti-parallel anti-parallel anti-parallel anti-parallel anti-parallel anti-parallel anti-parallel A PHE 44 A PHE 44 A HIS 47 A HIS 47 A ALA 121 A ALA 121 A HIS 125 A HIS 125 A ARG 144 A ARG 144 A VAL 149 A VAL 149 A ASP 2 A ASP 2 A ASP 9 A ASP 9 A PRO 15 A PRO 15 A ASN 24 A ASN 24 A GLY 27 A GLY 27 A LEU 34 A LEU 34 A VAL 107 A VAL 107 A ALA 109 A ALA 109 A GLY 40 A GLY 40 A HIS 42 A HIS 42 A LEU 95 A LEU 95 A VAL 97 A VAL 97 A SER 55 A SER 55 A LYS 57 A LYS 57 A LYS 60 A LYS 60 A VAL 62 A VAL 62 BINDING SITE FOR RESIDUE ZN A1152 Software 4 BINDING SITE FOR RESIDUE CU A1153 Software 4 A HIS 70 A HIS 70 4 1_555 A HIS 79 A HIS 79 4 1_555 A HIS 88 A HIS 88 4 1_555 A ASP 91 A ASP 91 4 1_555 A HIS 45 A HIS 45 4 1_555 A HIS 47 A HIS 47 4 1_555 A HIS 70 A HIS 70 4 1_555 A HIS 125 A HIS 125 4 1_555 155 H 3 2