1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 Kwan, A.H.Y. Gell, D.A. Verger, A. Crossley, M. Matthews, J.M. Mackay, J.P. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 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 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 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 structure STRUE6 2005 0969-2126 11 803 813 10.1016/S0969-2126(03)00122-9 12842043 Engineering a Protein Scaffold from a PHD Finger 2003 10.2210/pdb1mm2/pdb pdb_00001mm2 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 SINGLE WAVELENGTH M 1 1.0 6689.790 Mi2-beta Mi2-beta (residues 446-501) 1 man polymer 65.409 ZINC ION 2 syn non-polymer Chromodomain helicase-DNA-binding protein 4 no no GPLGSDHHMEFCRVCKDGGELLCCDTCPSSYHIHCLNPPLPEIPNGEWLCPRCTCPALKGK GPLGSDHHMEFCRVCKDGGELLCCDTCPSSYHIHCLNPPLPEIPNGEWLCPRCTCPALKGK 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 human Homo Escherichia Escherichia coli sample CHD4 9606 Homo sapiens 469008 Escherichia coli BL21(DE3) BL21 (DE3) PLASMID pGEX-6P database_2 pdbx_nmr_software pdbx_struct_assembly pdbx_struct_conn_angle pdbx_struct_oper_list struct_conn struct_ref_seq_dif struct_site repository Initial release Version format compliance Version format compliance Data collection Database references Derived calculations 1 0 2003-07-22 1 1 2008-04-28 1 2 2011-07-13 1 3 2022-02-23 _database_2.pdbx_DOI _database_2.pdbx_database_accession _pdbx_nmr_software.name _pdbx_struct_conn_angle.ptnr1_auth_comp_id _pdbx_struct_conn_angle.ptnr1_auth_seq_id _pdbx_struct_conn_angle.ptnr1_label_atom_id _pdbx_struct_conn_angle.ptnr1_label_comp_id _pdbx_struct_conn_angle.ptnr1_label_seq_id _pdbx_struct_conn_angle.ptnr3_auth_comp_id _pdbx_struct_conn_angle.ptnr3_auth_seq_id _pdbx_struct_conn_angle.ptnr3_label_atom_id _pdbx_struct_conn_angle.ptnr3_label_comp_id _pdbx_struct_conn_angle.ptnr3_label_seq_id _pdbx_struct_conn_angle.value _struct_conn.pdbx_dist_value _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_ref_seq_dif.details _struct_site.pdbx_auth_asym_id _struct_site.pdbx_auth_comp_id _struct_site.pdbx_auth_seq_id 1FP0 contains PHD domain from KAP-1 1F62 contains PHD domain from WSTF 1MM3 contains the 2nd PHD domain from Mi2b with C-terminal loop replaced by corresponding loop from WSTF RCSB Y PDBJ 2002-09-02 REL REL ZN ZINC ION This structure was determined mostly using standard 2D homonuclear techniques structures with the lowest energy 500 20 2D NOESY 2D TOCSY DQF-COSY N15-HSQC 7.5 ambient 298 K Structure calculations were performed using the package ARIA1.1 (Ambiguous Restraints in Iterative Assignment). Final structures are based on 1284 unambiguous NOE-derived distance constraints, 8 sets of ambiguous NOE-derived distance constraints and 39 additional dihedral angle restraints. simulated annealing, molecular dynamics, torsion angle dynamics 1 lowest energy 1mM Mi2-PHD2 protein, 1mM DTT, 10mM sodium phosphate buffer (pH 7.5), 150mM NaCl, 95% H2O, 5% D2O 95% H2O/5% D2O 0.2mM N15-labelled Mi2-PHD2 protein, 1mM DTT, 10mM sodium phosphate buffer (pH 7.5), 150mM NaCl, 95% H2O, 5% D2O 95% H2O/5% D2O Bruker processing XwinNMR 2.5 Bartels et al data analysis XEASY 1.3.13 Guntert et al refinement DYANA 1.5 Linge et al structure solution ARIA 1.1.2 600 Bruker DRX ZN 62 2 ZN ZN 62 A ZN 63 2 ZN ZN 63 A GLY 1 n 1 GLY 1 A PRO 2 n 2 PRO 2 A LEU 3 n 3 LEU 3 A GLY 4 n 4 GLY 4 A SER 5 n 5 SER 5 A ASP 6 n 6 ASP 6 A HIS 7 n 7 HIS 7 A HIS 8 n 8 HIS 8 A MET 9 n 9 MET 9 A GLU 10 n 10 GLU 10 A PHE 11 n 11 PHE 11 A CYS 12 n 12 CYS 12 A ARG 13 n 13 ARG 13 A VAL 14 n 14 VAL 14 A CYS 15 n 15 CYS 15 A LYS 16 n 16 LYS 16 A ASP 17 n 17 ASP 17 A GLY 18 n 18 GLY 18 A GLY 19 n 19 GLY 19 A GLU 20 n 20 GLU 20 A LEU 21 n 21 LEU 21 A LEU 22 n 22 LEU 22 A CYS 23 n 23 CYS 23 A CYS 24 n 24 CYS 24 A ASP 25 n 25 ASP 25 A THR 26 n 26 THR 26 A CYS 27 n 27 CYS 27 A PRO 28 n 28 PRO 28 A SER 29 n 29 SER 29 A SER 30 n 30 SER 30 A TYR 31 n 31 TYR 31 A HIS 32 n 32 HIS 32 A ILE 33 n 33 ILE 33 A HIS 34 n 34 HIS 34 A CYS 35 n 35 CYS 35 A LEU 36 n 36 LEU 36 A ASN 37 n 37 ASN 37 A PRO 38 n 38 PRO 38 A PRO 39 n 39 PRO 39 A LEU 40 n 40 LEU 40 A PRO 41 n 41 PRO 41 A GLU 42 n 42 GLU 42 A ILE 43 n 43 ILE 43 A PRO 44 n 44 PRO 44 A ASN 45 n 45 ASN 45 A GLY 46 n 46 GLY 46 A GLU 47 n 47 GLU 47 A TRP 48 n 48 TRP 48 A LEU 49 n 49 LEU 49 A CYS 50 n 50 CYS 50 A PRO 51 n 51 PRO 51 A ARG 52 n 52 ARG 52 A CYS 53 n 53 CYS 53 A THR 54 n 54 THR 54 A CYS 55 n 55 CYS 55 A PRO 56 n 56 PRO 56 A ALA 57 n 57 ALA 57 A LEU 58 n 58 LEU 58 A LYS 59 n 59 LYS 59 A GLY 60 n 60 GLY 60 A LYS 61 n 61 LYS 61 A author_defined_assembly 1 monomeric A CYS 12 A SG CYS 12 1_555 A ZN 63 C ZN ZN 1_555 A CYS 15 A SG CYS 15 1_555 108.5 A CYS 12 A SG CYS 12 1_555 A ZN 63 C ZN ZN 1_555 A HIS 32 A ND1 HIS 32 1_555 109.0 A CYS 15 A SG CYS 15 1_555 A ZN 63 C ZN ZN 1_555 A HIS 32 A ND1 HIS 32 1_555 108.5 A CYS 12 A SG CYS 12 1_555 A ZN 63 C ZN ZN 1_555 A CYS 35 A SG CYS 35 1_555 111.3 A CYS 15 A SG CYS 15 1_555 A ZN 63 C ZN ZN 1_555 A CYS 35 A SG CYS 35 1_555 109.4 A HIS 32 A ND1 HIS 32 1_555 A ZN 63 C ZN ZN 1_555 A CYS 35 A SG CYS 35 1_555 110.1 A CYS 24 A SG CYS 24 1_555 A ZN 62 B ZN ZN 1_555 A CYS 27 A SG CYS 27 1_555 109.3 A CYS 24 A SG CYS 24 1_555 A ZN 62 B ZN ZN 1_555 A CYS 50 A SG CYS 50 1_555 111.8 A CYS 27 A SG CYS 27 1_555 A ZN 62 B ZN ZN 1_555 A CYS 50 A SG CYS 50 1_555 108.8 A CYS 24 A SG CYS 24 1_555 A ZN 62 B ZN ZN 1_555 A CYS 53 A SG CYS 53 1_555 109.4 A CYS 27 A SG CYS 27 1_555 A ZN 62 B ZN ZN 1_555 A CYS 53 A SG CYS 53 1_555 107.8 A CYS 50 A SG CYS 50 1_555 A ZN 62 B ZN ZN 1_555 A CYS 53 A SG CYS 53 1_555 109.6 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 A HG ZN CYS ZN 12 63 1.06 1 A A HB2 HB3 CYS CYS 24 50 1.28 1 A A HB2 HB3 ARG LEU 52 58 1.30 2 A A HG ZN CYS ZN 12 63 1.40 4 A A HG ZN CYS ZN 12 63 1.06 5 A A HB2 HB3 CYS CYS 24 50 1.34 6 A A HB2 HE CYS ARG 50 52 1.33 7 A A HG ZN CYS ZN 12 63 1.26 8 A A HG ZN CYS ZN 12 63 1.12 9 A A HG ZN CYS ZN 12 63 1.06 11 A A HG ZN CYS ZN 12 63 1.20 13 A A HG ZN CYS ZN 12 63 1.13 16 A A HG ZN CYS ZN 12 63 1.08 16 A A HD2 HH2 TYR TRP 31 48 1.29 18 A A HG ZN CYS ZN 12 63 1.15 18 A A HB2 HE CYS ARG 50 52 1.19 18 A A HD2 HH2 TYR TRP 31 48 1.31 19 A A HG ZN CYS ZN 12 63 1.02 19 A A HB2 HB3 CYS CYS 24 50 1.23 19 A A HB2 H HIS HIS 7 8 1.35 20 A A HG ZN CYS ZN 12 63 1.36 1 A ASP 6 -171.67 -169.78 1 A HIS 8 62.66 -131.40 1 A VAL 14 -99.88 -62.07 1 A PRO 28 -75.32 38.18 1 A TYR 31 -117.20 -146.52 1 A PRO 51 -69.91 10.41 1 A PRO 56 -79.17 44.18 1 A ALA 57 -162.72 -163.65 2 A ASP 6 -89.40 -132.89 2 A THR 26 -106.08 -61.58 2 A TYR 31 -127.33 -161.51 2 A HIS 32 -123.07 -130.25 2 A HIS 34 -143.46 -3.14 2 A CYS 50 -48.51 159.85 2 A ALA 57 -109.16 46.33 3 A PRO 28 -81.56 40.79 3 A TYR 31 -131.44 -153.43 3 A LEU 36 -125.72 -166.57 3 A CYS 50 -46.92 159.32 3 A PRO 51 -66.30 34.57 3 A ARG 52 -141.75 -47.18 3 A CYS 55 53.30 71.41 4 A LEU 3 67.95 -74.55 4 A SER 5 -95.65 48.98 4 A CYS 12 48.16 -109.06 4 A ARG 13 -179.06 -55.00 4 A ASP 17 168.31 -138.72 4 A HIS 32 -128.96 -125.08 4 A LYS 59 -165.27 106.75 5 A HIS 7 70.34 -67.36 5 A PRO 28 -82.46 34.29 5 A TYR 31 -130.87 -152.95 5 A HIS 32 -134.38 -138.17 5 A PRO 51 -66.99 13.76 5 A ALA 57 -143.73 32.93 5 A LYS 59 -147.06 29.54 6 A HIS 8 68.68 -102.30 6 A PRO 28 -88.22 48.33 6 A TYR 31 -133.35 -159.64 6 A LEU 36 -118.13 -166.21 6 A PRO 51 -66.46 42.25 6 A ARG 52 -151.29 -29.79 6 A CYS 55 74.22 146.22 7 A SER 5 -95.45 -68.51 7 A HIS 8 62.79 -120.07 7 A VAL 14 -138.22 -47.92 7 A TYR 31 -128.80 -162.10 7 A GLU 47 -99.73 59.98 7 A PRO 51 -68.03 16.02 8 A LEU 3 64.58 -164.88 8 A SER 5 -140.79 -45.95 8 A ASP 6 -172.79 -138.85 8 A HIS 8 70.93 -175.84 8 A THR 26 -121.57 -54.00 8 A PRO 28 -78.36 48.42 8 A TYR 31 -124.87 -156.15 8 A LEU 36 -123.32 -166.45 8 A THR 54 -63.25 -78.42 9 A SER 5 -85.14 -76.91 9 A ASP 6 -150.99 -91.63 9 A HIS 8 55.97 -129.79 9 A VAL 14 -103.51 -65.92 9 A PRO 28 -74.87 38.26 9 A TYR 31 -117.02 -152.41 9 A HIS 32 -129.77 -160.46 9 A CYS 50 -40.36 158.63 10 A HIS 7 -152.07 -44.52 10 A HIS 8 50.39 -137.46 10 A THR 26 -120.93 -63.77 10 A PRO 28 -96.36 30.84 10 A LEU 36 -116.06 -158.54 10 A PRO 51 -67.57 37.95 10 A ARG 52 -146.66 -45.17 10 A THR 54 -65.06 74.31 10 A CYS 55 -175.90 133.22 11 A ASP 6 -115.16 -148.78 11 A HIS 7 61.26 -136.77 11 A VAL 14 -144.36 -49.55 11 A LYS 16 75.14 -0.97 11 A THR 26 -124.48 -52.52 11 A TYR 31 -125.70 -161.52 11 A HIS 32 -134.35 -146.28 11 A PRO 44 -67.38 93.97 11 A PRO 51 -70.46 34.87 11 A ARG 52 -140.38 -48.66 11 A CYS 55 -160.92 85.99 11 A LEU 58 -121.50 -51.39 11 A LYS 59 -146.17 54.44 12 A HIS 7 -147.62 11.14 12 A PRO 28 -92.32 32.51 12 A HIS 32 -126.07 -133.30 12 A CYS 55 65.24 101.36 12 A PRO 56 -66.83 -76.01 13 A HIS 7 -167.47 -55.23 13 A PRO 28 -89.03 33.06 13 A TYR 31 -127.04 -154.31 13 A LEU 36 -105.69 -164.16 13 A LEU 49 69.08 130.39 14 A TYR 31 -129.23 -155.33 14 A CYS 50 -42.00 155.07 15 A LEU 3 69.83 -69.68 15 A ASP 6 -119.80 -72.72 15 A HIS 7 56.05 -110.71 15 A PRO 28 -95.27 40.47 15 A TYR 31 -129.72 -166.51 15 A HIS 32 -120.59 -127.73 15 A PRO 51 -70.23 33.57 15 A ARG 52 -137.56 -36.29 15 A CYS 55 73.79 114.38 16 A ASP 6 -96.19 -60.08 16 A HIS 7 65.06 97.60 16 A HIS 8 63.58 -124.64 16 A ARG 13 -75.49 46.81 16 A VAL 14 -136.63 -33.10 16 A PRO 28 -78.51 39.62 16 A TYR 31 -125.07 -154.01 16 A LEU 36 -150.06 -67.18 16 A CYS 50 -47.44 162.28 16 A ALA 57 -104.34 63.23 16 A LYS 59 69.37 -170.90 17 A HIS 8 62.38 -99.74 17 A ASP 17 -166.99 -154.64 17 A TYR 31 -128.78 -152.23 17 A HIS 32 -143.66 -157.03 17 A LEU 36 -126.34 -157.81 18 A SER 5 71.05 -50.17 18 A VAL 14 -79.59 -73.16 18 A TYR 31 -126.67 -159.06 18 A PRO 51 -66.48 50.33 18 A ARG 52 -166.21 -22.03 18 A PRO 56 -50.12 109.30 19 A HIS 7 -86.66 -124.89 19 A HIS 8 69.46 -100.87 19 A PHE 11 -124.15 -74.30 19 A CYS 12 159.35 138.39 19 A TYR 31 -126.01 -155.99 19 A HIS 32 -128.67 -129.75 19 A LEU 58 74.10 -45.81 19 A LYS 59 69.65 -66.79 20 A ASP 6 -167.88 -149.40 20 A CYS 12 -62.86 -79.19 20 A ARG 13 179.24 -48.88 20 A THR 26 -122.45 -53.46 20 A HIS 32 -126.77 -121.53 20 A HIS 34 -155.92 8.32 20 A CYS 50 -49.62 161.56 20 A PRO 51 -66.86 39.42 20 A ARG 52 -149.67 -39.02 Solution structure of the 2nd PHD domain from Mi2b 1 N N 2 N N 2 N N metalc 2.241 A CYS 12 A SG CYS 12 1_555 A ZN 63 C ZN ZN 1_555 metalc 2.287 A CYS 15 A SG CYS 15 1_555 A ZN 63 C ZN ZN 1_555 metalc 2.318 A CYS 24 A SG CYS 24 1_555 A ZN 62 B ZN ZN 1_555 metalc 2.272 A CYS 27 A SG CYS 27 1_555 A ZN 62 B ZN ZN 1_555 metalc 1.961 A HIS 32 A ND1 HIS 32 1_555 A ZN 63 C ZN ZN 1_555 metalc 2.327 A CYS 35 A SG CYS 35 1_555 A ZN 63 C ZN ZN 1_555 metalc 2.287 A CYS 50 A SG CYS 50 1_555 A ZN 62 B ZN ZN 1_555 metalc 2.279 A CYS 53 A SG CYS 53 1_555 A ZN 62 B ZN ZN 1_555 DNA BINDING PROTEIN PHD, zinc finger, protein scaffold, DNA binding protein CHD4_HUMAN UNP 1 446 Q14839 DHHMEFCRVCKDGGELLCCDTCPSSYHIHCLNPPLPEIPNGEWLCPRCTCPALKGK 446 501 1MM2 6 61 Q14839 A 1 6 61 1 cloning artifact GLY 1 1MM2 A Q14839 UNP 1 1 cloning artifact PRO 2 1MM2 A Q14839 UNP 2 1 cloning artifact LEU 3 1MM2 A Q14839 UNP 3 1 cloning artifact GLY 4 1MM2 A Q14839 UNP 4 1 cloning artifact SER 5 1MM2 A Q14839 UNP 5 BINDING SITE FOR RESIDUE ZN A 62 A ZN 62 Software 4 BINDING SITE FOR RESIDUE ZN A 63 A ZN 63 Software 4 A CYS 24 A CYS 24 4 1_555 A CYS 27 A CYS 27 4 1_555 A CYS 50 A CYS 50 4 1_555 A CYS 53 A CYS 53 4 1_555 A CYS 12 A CYS 12 4 1_555 A CYS 15 A CYS 15 4 1_555 A HIS 32 A HIS 32 4 1_555 A CYS 35 A CYS 35 4 1_555