Structure of human DNA polymerase beta Host-Guest complex with the dG base paired with a dG

PDB ID: 5DBC
Metal site ID: 5DBC-NA-1
Bound amino acids or nucleotide residues: G1I1T1V1
Group identifier: G2I1R1S1V1
Is homomeric: False
Amino acid or nucleotide residue IDs: DG P.9 ILE A.106 THR A.101 VAL A.103
All ligands IDs: DG P.9 HOH P.102 HOH P.107 ILE A.106 THR A.101 VAL A.103
Number of coordinating amino acids or nucleotide residues: 4
Number of coordinating ligands: 6
Number of coordinating chains: 2
Number of coordinating chains: 2
Representative metal site in the group: 1ZQI-K-1
Similar binding_sites:
Metal site idBound amino acidsBound ligands IDs
1BPY-NA-1G1I1T1V1 DG P.9 ILE A.106 THR A.101 VAL A.103
1BPZ-NA-1G1I1T1V1 DG P.9 HOH A.500 ILE A.106 THR A.101 VAL A.103
1ZJM-NA-1G1I1T1V1 DG P.4 DT P.3 HOH P.914 HOH P.932 HOH T.32
1ZQA-K-1I1T2V1 DT P.6 HOH A.601 HOH P.665 ILE A.106 THR A.101 VAL A.103
1ZQG-NA-1I1T2V1 DT P.6 HOH A.601 ILE A.106 THR A.101 VAL A.103
1ZQK-K-1I1T2V1 DT P.6 HOH P.601 ILE A.106 THR A.101 VAL A.103
1ZQO-NA-1I1T2V1 DT P.6 HOH P.601 ILE A.106 THR A.101 VAL A.103
1ZQS-NA-1I1T2V1 DT P.6 HOH A.601 ILE A.106 THR A.101 VAL A.103
2I9G-NA-1G1I1T1V1 DG P.9 HOH A.512 HOH P.508 ILE A.106 THR A.101 VAL A.103
2ISO-NA-1G1I1T1V1 ASP A.190 ASP A.192 ASP A.256 GFF A.338 HOH P.427
2ISP-NA-1G1I1T1V1 DG P.9 HOH A.562 HOH P.188 ILE A.106 THR A.101 VAL A.103
2P66-NA-1G1I1T1V1 DG C.9 HOH C.344 HOH C.347 ILE A.106 THR A.101 VAL A.103
3RJE-NA-1G1I1T1V1 DG P.9 HOH P.11 HOH P.67 ILE A.106 THR A.101 VAL A.103
3RJG-NA-1G1I1T1V1 DG P.9 HOH P.11 HOH P.20 ILE A.106 THR A.101 VAL A.103
3RJJ-NA-1G1I1T1V1 DG P.9 HOH A.342 HOH P.26 ILE A.106 THR A.101 VAL A.103
4DO9-NA-1G1I1T1V1 DG P.9 HOH P.101 ILE A.106 THR A.101 VAL A.103
4DOA-NA-1G1I1T1V1 DG P.9 HOH P.101 ILE A.106 THR A.101 VAL A.103
4DOB-NA-1G1I1T1V1 DG P.9 HOH P.101 ILE A.106 THR A.101 VAL A.103
4F5N-NA-1G1I1T1V1 HOH A.502 HOH A.517 HOH A.819 HOH P.101 THR A.101
4KLG-NA-2G1I1T1V1 ASP A.190 ASP A.192 ASP A.256 DC P.10 DC P.11
4KLJ-NA-1G1I1T1V1 DG P.9 HOH A.799 HOH P.203 ILE A.106 THR A.101 VAL A.103
4KLL-NA-2G1I1T1V1 DC D.3 HOH A.595 HOH D.103 LEU A.62 LYS A.60 VAL A.65
4KLM-NA-2G1I1T1V1 DG P.9 HOH A.548 HOH P.102 ILE A.106 THR A.101 VAL A.103
4KLO-NA-3G1I1T1V1 DG P.9 HOH A.837 HOH P.202 ILE A.106 THR A.101 VAL A.103
4M2Y-NA-1G1I1T1V1 DG P.9 HOH P.101 ILE A.106 THR A.101 VAL A.103
4M9G-NA-2G1I1T1V1 DG P.9 HOH A.513 HOH P.105 ILE A.106 THR A.101 VAL A.103
4MF2-NA-1G1I1T1V1 DG P.9 HOH P.101 ILE A.106 THR A.101 VAL A.103
4O5C-NA-1G1I1T1V1 DG P.9 HOH P.101 ILE A.106 THR A.101 VAL A.103
4PGY-NA-1G1I1T1V1 DG P.9 HOH A.522 ILE A.106 THR A.101 VAL A.103
4PPX-NA-2G1I1T1V1 DG P.9 HOH A.521 HOH P.101 ILE A.106 THR A.101 VAL A.103
4R63-NA-1G1I1T1V1 DG P.9 HOH A.503 HOH P.101 ILE A.106 THR A.101 VAL A.103
4R64-NA-1G1I1T1V1 DG P.9 HOH A.641 HOH P.119 ILE A.106 THR A.101 VAL A.103
4RQ1-NA-1G1I1T1V1 DG P.9 HOH A.502 ILE A.106 THR A.101 VAL A.103
4YMM-NA-1G1I1T1V1 DG P.9 HOH A.574 HOH P.103 ILE A.106 THR A.101 VAL A.103
4Z6D-NA-2G1I1T1V1 DG P.9 HOH P.111 ILE A.106 THR A.101 VAL A.103
5BOL-NA-1G1I1T1V1 DG P.9 HOH A.721 HOH P.501 ILE A.106 THR A.101 VAL A.103
5BOM-NA-1G1I1T1V1 DG P.9 HOH A.661 HOH P.105 ILE A.106 THR A.101 VAL A.103
5DB6-NA-1G1I1T1 DG P.9 HOH A.505 ILE A.106 THR A.101
5DB8-NA-1G1I1T1V1 DG P.9 HOH A.515 HOH P.104 ILE A.106 THR A.101 VAL A.103
5DBA-NA-1G1I1T1V1 DG P.9 HOH A.600 HOH P.110 ILE A.106 THR A.101 VAL A.103
5DBC-NA-1G1I1T1V1 DG P.9 HOH P.102 HOH P.107 ILE A.106 THR A.101 VAL A.103
5HHI-NA-1I1T2V1 DT P.9 HOH P.206 ILE A.106 THR A.101 VAL A.103
5J0O-NA-1G1I1T1V1 DG P.9 HOH A.722 HOH P.110 ILE A.106 THR A.101 VAL A.103
5J0P-NA-1G1I1T1V1 DG P.9 HOH A.566 HOH P.103 ILE A.106 THR A.101 VAL A.103
5J0S-NA-1G1I1T1V1 DG P.9 HOH A.753 HOH P.114 ILE A.106 THR A.101 VAL A.103
5J0U-NA-1G1I1T1V1 DG P.9 HOH A.733 HOH P.116 ILE A.106 THR A.101 VAL A.103
5J0W-NA-1G1I1T1V1 DG P.9 HOH A.628 HOH P.107 ILE A.106 THR A.101 VAL A.103
5J0Y-NA-1G1I1T1V1 DG P.9 HOH A.765 HOH P.204 ILE A.106 THR A.101 VAL A.103
5J29-NA-1G1I1T1V1 DG P.9 HOH P.105 HOH P.115 ILE A.106 THR A.101 VAL A.103
5J2A-NA-1G1I1T1 DG P.9 HOH A.551 ILE A.106 THR A.101
5J2B-NA-1G1I1T1V1 DG P.9 HOH A.666 HOH P.104 ILE A.106 THR A.101 VAL A.103
5J2C-NA-1G1I1T1V1 DG P.9 HOH A.720 HOH P.104 ILE A.106 THR A.101 VAL A.103
5J2D-NA-1G1I1T1V1 DG P.9 HOH A.728 HOH P.110 ILE A.106 THR A.101 VAL A.103
5J2E-NA-1G1I1T1V1 DG P.9 HOH A.683 HOH P.106 ILE A.106 THR A.101 VAL A.103
5J2F-NA-1G1I1T1V1 DG P.9 HOH A.745 HOH P.107 ILE A.106 THR A.101 VAL A.103
5J2I-NA-1G1I1T1V1 DG P.9 HOH A.661 HOH P.106 ILE A.106 THR A.101 VAL A.103
5J2J-NA-1G1I1T1V1 DG P.9 HOH A.718 HOH P.107 ILE A.106 THR A.101 VAL A.103
5J2K-NA-1G1I1T1V1 DG P.9 HOH P.105 ILE A.106 THR A.101 VAL A.103
5TBA-NA-1G1I1T1V1 DG P.9 HOH A.538 HOH P.103 ILE A.106 THR A.101 VAL A.103
5TBC-NA-1G1I1T1V1 DG P.9 HOH A.561 HOH A.572 ILE A.106 THR A.101 VAL A.103
5U8H-NA-2G1I1T1V1 DG P.9 HOH A.637 HOH P.118 ILE A.106 THR A.101 VAL A.103
5U8I-NA-2G1I1T1V1 DG P.9 HOH A.547 HOH P.104 ILE A.106 THR A.101 VAL A.103
5V1I-NA-1G1I1T1V1 DG P.9 HOH A.674 HOH P.201 ILE A.106 THR A.101 VAL A.103
5V1J-NA-1G1I1T1V1 DG P.9 HOH A.517 HOH P.101 ILE A.106 THR A.101 VAL A.103
5V1P-NA-1G1I1T1V1 DG P.9 HOH A.695 HOH P.504 ILE A.106 THR A.101 VAL A.103
5VEZ-NA-1G1I1T1V1 DG P.9 HOH A.682 HOH P.202 ILE A.106 THR A.101 VAL A.103
5VS0-MG-3C1I1T1V1 DC P.9 HOH A.589 HOH P.201 ILE A.106 THR A.101 VAL A.103
5VS2-CA-2C1I1T1V1 DC P.9 HOH A.609 ILE A.106 THR A.101 VAL A.103
6BEL-NA-1G1I1T1V1 DG P.9 HOH A.810 HOH P.104 ILE A.106 THR A.101 VAL A.103
6BTE-NA-1G1I1T1V1 DG P.9 HOH A.758 HOH P.106 ILE A.106 THR A.101 VAL A.103
6CR3-NA-1G1I1T1V1 DG P.9 HOH A.803 HOH P.106 ILE A.106 THR A.101 VAL A.103
6CR5-NA-1G1I1T1V1 DG P.9 HOH P.102 HOH P.110 ILE A.106 THR A.101 VAL A.103
6CR6-NA-1G1I1T1V1 DG P.9 HOH P.206 HOH P.211 ILE A.106 THR A.101 VAL A.103
6CR7-NA-1G1I1T1V1 DG P.9 HOH P.110 ILE A.106 THR A.101 VAL A.103
6CR8-NA-1G1I1T1V1 DG P.9 HOH A.709 HOH P.106 ILE A.106 THR A.101 VAL A.103
6CR9-NA-1G1I1T1V1 DG P.9 HOH A.771 HOH P.106 ILE A.106 THR A.101 VAL A.103
6CRB-NA-1G1I1T1V1 DG P.9 HOH A.611 HOH P.103 ILE A.106 THR A.101 VAL A.103
6CRC-NA-1G1I1T1V1 DG P.9 ILE A.106 THR A.101 VAL A.103
6E3R-NA-1G1I1T1V1 DG P.9 HOH A.505 HOH P.106 HOH P.112 ILE A.106 THR A.101 VAL A.103
6N2T-NA-1G1I1T1V1 DG P.9 HOH A.536 HOH P.102 ILE A.106 THR A.101 VAL A.103
6NKT-NA-1G1I1T1V1 DG P.9 HOH A.530 ILE A.106 THR A.101 VAL A.103
6NKU-NA-1I1T2V1 DT P.9 HOH P.203 ILE A.106 THR A.101 VAL A.103
6NKZ-NA-1I1T2V1 DT P.9 HOH A.715 HOH P.202 ILE A.106 THR A.101 VAL A.103
6PKZ-NA-1G1I1T1V1 DG P.9 HOH A.539 HOH P.101 ILE A.106 THR A.101 VAL A.103
6U2O-NA-1G1I1T1V1 DG P.9 HOH P.106 ILE A.106 THR A.101 VAL A.103
7MZ0-NA-1G1I1T1V1 DG P.9 HOH A.594 ILE A.106 THR A.101 VAL A.103
7RBE-NA-1G1I1T1V1 DG P.9 HOH A.716 HOH P.115 ILE A.106 THR A.101 VAL A.103
7RBG-CA-2G1I1T1V1 DG P.9 HOH A.668 HOH P.102 ILE A.106 THR A.101 VAL A.103
8ICB-NA-1I1T2V1 DT P.6 HOH A.601 ILE A.106 THR A.101 VAL A.103
8ICH-NA-1I1T2V1 DT P.6 HOH A.601 ILE A.106 THR A.101 VAL A.103
8ICI-NA-1I1T2V1 DT P.6 HOH A.601 ILE A.106 THR A.101 VAL A.103
8ICL-NA-1I1T2V1 DT P.6 HOH A.601 ILE A.106 THR A.101 VAL A.103
8ICM-NA-1I1T2V1 DT P.6 HOH A.601 ILE A.106 THR A.101 VAL A.103
8ICZ-NA-1I1T2V1 DT P.6 HOH P.601 ILE A.106 THR A.101 VAL A.103
9ICC-NA-1I1T2V1 DT P.6 HOH A.601 ILE A.106 THR A.101 VAL A.103