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Dealing with metals
We are updating metal-containing entries using a newly developed mechanism:
acedrg -c input.cif -o ${out}
metalCoord update -i ${out}_final.cif -o ${out}_mc.cif
servalcat refine_geom --update_dictionary ${out}_mc.cifHowever, in many cases CCD's cif files need corrections. Major correction types are:
- All sandwich and half sandwich had errors in bond orders, charges or hydrogen atoms
- C-O triple bonds were replaced with double bonds
- Metal-metal bonds were removed
- Some haem like structures have been corrected. They may need to be dealt with again.
- In many metal containing components there are some atoms as place holders. They are replaced with protein atoms within the molecule. We changed only some of them. Perhaps for all of them we should remove place holders.
The following is the list of corrections we made so far
| ID | correction |
|---|---|
| 067 | Sandwich, missing H atoms and charge on rings |
| 2T8 | C-O triple bond should be double |
| 498 | Sandwich, missing H atoms and charge |
| 4IR | Half sandwich, bond orders and charge are missing |
| 4WV | C-O triple bond should be double |
| 4WW | C-O triple bond should be double |
| 4WX | C-O triple bond should be double |
| 670 | Sandwich, missing H atoms and charge on rings |
| 7G4 | Sandwich, bond orders and charges |
| 82N | Metal-metal bond should be removed |
| 84A | Sandwich, missing H atoms and charge on rings |
| 8CY | Sandwich, missing H atoms and charge on rings |
| 8TH | Half sandwich, bond orders and charge |
| 9Q8 | C-O triple bond should be double |
| 9SQ | C-O triple bond should be double |
| 9UX | delete hydrogen |
| AG1 | C-O triple bond should be double |
| B13 | Problem in pyrroles |
| B1R | Sandwich, missing H atoms and charge on rings |
| B9F | Sandwich, missing H atoms and charge on rings |
| BE7 | CL1 should be removed (it is a general problem) |
| C4R | H atoms on C atoms bonded to the metal |
| CFC | Sandwich, missing charge on rings, wrong bond order |
| CJI | metal-metal bond should be removed |
| CUA | metal-metal bond should be removed |
| CUZ | metal-metal bond should be removed |
| CWO | Double bond for P-O bond should be added |
| CZL | Wrong H atoms on S and metal-metal bonds should be removed |
| D3I | metal-metal |
| D5A | metal-metal |
| DW1 | C-O triple bond should be double. RU to C12/C13/C14/C16/C17 bonds are needed |
| DW2 | C-O triple bond should be double |
| DWC | Half sandwich, bond orders and charge |
| E52 | Half sandwich, charge |
| F3I | metal-metal |
| F5I | metal-metal |
| F5T | metal-metal |
| FE9 | O1/S1/HS1/H2 should be removed to make it consistent with the PDB |
| FLL | C-O triple bond should be double |
| FNE | C-O triple bond should be double |
| FS2 | metal-metal; bonding pattern should be checked |
| FSX | metal-metal |
| FU8 | C-O triple bond should be double |
| G9R | Missing metal pyrrole bond |
| GXW | double bond for P-O bond |
| GXZ | double bond for P-O bond |
| H57 | Sandwich, metal ring bonds, H atoms and charge |
| H58 | Sandwich, metal ring bonds, H atoms and charge |
| H79 | Sandwich, missing charge on rings, wrong bond order |
| HB1 | Half sandwich, bond orders and charge |
| HBF | Sandwich, missing charge on rings, wrong bond order |
| HC0 | Metal-metal |
| HC1 | Metal-metal |
| HCO | Bond orders on pyrrole |
| HEC | wrong chemistry. HEM should be used |
| HDD | Bond orders on pyrrole |
| HDE | Bond orders on pyrrole |
| HE5 | Bond orders on pyrrole |
| HFM | bond orders on pyrrole |
| HFW | double bond for P-O bond |
| HRU | Half sandwich, bond orders |
| ISW | One of the pyrroles had wrong H atom |
| J0K | Half sandwich, bond orders, charge |
| J0N | Half sandwich, bond orders, charge |
| J52 | C-O triple bond should be double |
| JCT | Half sandwich, bond orders, charge |
| JGH | double bond for P-O bond |
| JM1 | Half sandwich, bond orders, charge |
| JR3 | Half sandwich, bond orders, charge |
| JSC | Sandwich, metal ring bonds, H atoms and charge |
| JSD | Sandwich, metal ring bonds, H atoms and charge |
| JSE | Sandwich, metal ring bonds, H atoms and charge |
| K3G | double bond for P-O bond |
| KEG | double bond for P-O bond |
| L8W | Sandwich, metal ring bonds, H atoms and charge |
| LFH | C-O triple bond should be double |
| LSI | Sandwich, metal ring bonds, H atoms and charge |
| ME3 | Half sandwich, bond orders, charge |
| MHX | C-O triple bond should be double |
| N7H | Fix nitro group |
| NFR | Metal-metal |
| NFU | Metal-metal |
| NFV | C-O triple bond should be double |
| NOF | Half sandwich, bond orders, charge |
| NT3 | N-O triple bond should be double |
| O1N | Half sandwich, H atoms, bond orders, charge |
| ORS | Half sandwich, bond orders, charge |
| OS1 | C-O triple bond should be double |
| OSV | C-S bond changed from triple to single, N-C bond from single to triple |
| OT1 | Half sandwich, bond orders, charge |
| PNQ | Nitro group: N-O bonds changed to double (these are equivalent) |
| PW9 | double bond for P-O bond |
| R1N | Half sandwich, bond orders, charge |
| R2I | Metal-metal |
| REI | C-O triple bond should be double |
| REJ | C-O triple bond should be double |
| REP | C-O triple bond should be double |
| REQ | C-O triple bond should be double |
| RMD | Half sandwich, bond orders, charge |
| RSW | Half sandwich, bond orders |
| RTC | C-O triple bond should be double |
| RU0 | Metal-metal |
| RU1 | C-O triple bond should be double |
| RU2 | C-O triple bond should be double |
| RUI | Half sandwich, H atoms, charge |
| RUX | C-O triple bond should be double |
| SRX | Half sandwich, bond orders, charge |
| TDJ | Sandwich, metal ring bonds, H atoms and charge |
| TPT | CL1 removed to make it consistent with the PDB |
| TZ6 | Metal-metal |
| UWE | C-O triple bond should be double |
| V7F | Add H atoms on N02 and N04 |
| VER | O in the larger ring of the porphyrin should have single bonds |
| VHR | C-O triple bond should be double |
| VKZ | Half sandwich, bond orders |
| VL2 | Half sandwich, bond orders |
| WO2 | double bond for P-O bond |
| YJT | Metal-metal |
| YMQ | Metal-metal |
| YWV | Metal-metal |
| ZJK | Metal-metal |
| ZJO | Metal-metal |
| ZKG | double bond for P-O bond |
| ZQ2 | Metal-metal |
| ZWH | Metal-metal |
| ZWO | Metal-metal |
| ZXE | Metal-metal |
HEC would never exist as an isolated ligand, but should always be linked to CYS residues. We fixed HEC bonding pattern and used charge -1 trick for CAC and CAB atoms. See https://github.com/MonomerLibrary/monomers/pull/60.
CYS-HEMB:
LINK: RES-NAME-1 CYS ATOM-NAME-1 SG RES-NAME-2 HEM ATOM-NAME-2 CAB CHANGE BOND CAB CBB SINGLE 2 FILE-2 ../HEM_mc_refined_updated.cif
CYS-HEMC:
LINK: RES-NAME-1 CYS ATOM-NAME-1 SG RES-NAME-2 HEM ATOM-NAME-2 CAC CHANGE BOND CAC CBC SINGLE 2 FILE-2 ../HEM_mc_refined_updated.cif
H31 should be renamed to H32.
HEC-CYS1:
LINK: RES-NAME-1 CYS ATOM-NAME-1 SG RES-NAME-2 HEC ATOM-NAME-2 CAC CHANGE CHARGE 2 CAC 0 FILE-2 ../AcedrgOut.cif
HEC-CYS2:
LINK: RES-NAME-1 CYS ATOM-NAME-1 SG RES-NAME-2 HEC ATOM-NAME-2 CAB CHANGE CHARGE 2 CAB 0 FILE-2 ../AcedrgOut.cif
The typical distances between metal sites and surrounding atoms are provided in the file metals.json. The data is organized by metal element, element of its interaction partner, and the metal's coordination number.
For instance, typical distance for iron-sulphur interaction, relevant for the Fe-S clusters, can be explored. We can select the section for "Fe" and its subsection "S" - open the file metals.json in a text editor or inpect it using the following Python commands:
import json
import pprint
with open('metals.json', 'r') as metals_file:
data = json.load(metals_file)
pprint.pprint(data['metal_coordination']['Fe']['S'])
We find out 7 possible coordination numbers, denoted as "coord": 3, 4, 5, 6, 7, 8 and 11. For each coordination number, the following information is provided:
- Median interatomic distance and its absolute deviation.
- Mean interatomic distance and its standard deviation.
- Number of reference structures where such coordination was observed, denoted as "count". In this example, note that the coordination numbers 7 and 11 are extremely rare, with only one reference structure for each, thus, the reported values for these coordination numbers may be misleading.
Let's focus on coordination number 6 which is the most common (752 reference structures).
coord_6 = next(c for c in data['metal_coordination']['Fe']['S'] if c['coord'] == 6)
pprint.pprint(coord_6)
Output:
{'coord': 6,
'count': 752,
'mad': 0.055011272422031965,
'mean': 2.354311549366653,
'median': 2.315759378691282,
'modes': [{'mode': 2.2918619816782826,
'std': 0.044788392111853155,
'weight': 0.7156127571039738},
{'mode': 2.5114554031426977,
'std': 0.07950441399256195,
'weight': 0.2843872428960263}],
'std': 0.1142177002047632}
There are two entries under the subsection "modes", indicating that two options for a typical interatomic distance, as multiple coordination classes are possible for the same coordination number. The "weight" of each mode refers to the ratio of reference structures with a particular mode. Thus, the ideal Fe-S interatomic distances, when considering iron with a coordination number of 6, are (2.29 ± 0.05) Å and (2.51 ± 0.08) Å as identified in 71.6 % and 28.4 % of the 752 reference structures, respectively.
Note: The records in the file metals.json are updated in time and could slightly change from January 2025, when this text was written.