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Re: Protein+Metal Ion?



Modeller Care wrote:
Non-member submission forwarded by the list-owner
--------------------------------------------------------------------------

I would like to model a protein that contains Zn in the active site.  In =
the template structure, two His residues are coordinated to the Zn.  The =
target sequence also has these residues and the sequences display > 50% =
identity.  How do I force the His residues to similarly coordinate the =
Zn in the modelled structure?  If the Zn atom is in .pdb file, modeller =
doesn't seem to notice.  Without the Zn atom present,  the His =
sidechains simply flop around in the active site (not surprisingly).

Marc Campitelli

Hi,
sounds familiar...
You need to:

i) put in the top file:
SET HETATM_IO =   on

ii)put in the end of the alignment that you will use to make the model (ali file):

/z/*

Note: I put the symbol z that describe Zn2+, but you have to take a look in the modlib directory.
The file name is restyp.lib taht look like this:
 

#     PDB-3               PDB-1 CHARMM    DESCRIPTION
#-----------------------------------------------------------------------------
  1 | ALA                 | A | ALA  | alanine
  2 | CYS CYS CSH         | C | CYS  | cysteine
  3 | ASP                 | D | ASP  | aspartic acid, +1
  4 | GLU                 | E | GLU  | glutamic acid, +1
  5 | PHE                 | F | PHE  | phenylalanine
  6 | GLY                 | G | GLY  | glycine
  7 | HIS                 | H | HSD  | histidine, neutral, proton on ND1
  8 | ILE                 | I | ILE  | isoleucine
  9 | LYS                 | K | LYS  | lysine, +1
 10 | LEU                 | L | LEU  | leucine
 11 | MET                 | M | MET  | methionine
 12 | ASN                 | N | ASN  | asparagine
 13 | PRO PR0 PRZ         | P | PRO  | proline
 14 | GLN                 | Q | GLN  | glutamine
 15 | ARG                 | R | ARG  | arginine, +1
 16 | SER                 | S | SER  | serine
 17 | THR                 | T | THR  | threonine
 18 | VAL                 | V | VAL  | valine
 19 | TRP                 | W | TRP  | tryptophan
 20 | TYR                 | Y | TYR  | tryrosine
 21 | GAP                 | - | GAP  | an alignment gap
 22 | ASX                 | B | ASX  | ASP/ASN ambiguous
 23 | GLX                 | Z | GLX  | GLU/GLN ambiguous
 24 | UNK                 | X | UNK  | unknown residue type
 25 | PCA PGA             | p | #### | pyrrolidine carboxylic acid (pyroglutamate)
 26 | HSE                 | 6 | HSE  | histidine, neutral, proton on NE2
 27 | HSP                 | 7 | HSP  | histidine, +1 (proton on NE2 and ND1)
 28 | HOH H2O OH2 MOH WAT | w | TIP3 | water
 29 | CAL CA              | 3 | CAL  | calcium ion, +2
 30 | ZN2                 | z | ZN2  | zinc, +2
 31 | HEM                 | h | HEME | heme ligand
 32 | NTR                 | n | NTER | patch for standard N-terminus, +1
 33 | GLP                 | # | GLYP | patch for glycine N-terminus
 34 | PRP                 | # | PROP | patch for proline N-terminus
 35 | ACE                 | e | ACE  | patch for acetylated N-terminus
 36 | TER                 | c | CTER | patch for standard C-terminus
 37 | CT1                 | # | CT1  | patch for methylated C-terminus from methyl acetate
 38 | CT2                 | # | CT2  | patch for amidated C-terminus
 39 | CT3                 | # | CT3  | patch for N-Methylamide C-terminus
 40 | ASP                 | # | ASPP | protonated aspartate, proton on OD2
 41 | GLU                 | # | GLUP | protonated glutamate, proton on OE2
 42 | LNK                 | # | LINK | patch for linkage of images or segments
 43 | DIS                 | # | DISU | patch for disulfide
 44 | HS2                 | # | HS2  | patch for neutr His, + from ND1 to NE2
 45 | O2                  | # | O2   | O2 ligand for heme
 46 | CO                  | # | CO   | CO ligand for heme
 47 | FHM                 | # | FHEM | patch for heme
 48 | PHM                 | # | PHEM | patch for heme
 49 | PLO                 | # | PLO2 | patch for heme
 50 | LIG                 | # | PLIG | patch for heme
 51 | LWA                 | # | PLWA | patch for heme
 52 | CYS CSS CYX         | C | CSS  | cystine
 53 | ABU                 | g | #### | amino-butyric acid
 54 | ACD                 | d | #### | acidic unknown
 55 | ALB                 | l | #### | beta-alanine
 56 | ALI                 | a | #### | aliphatic unknown
 57 | ARO                 | r | #### | aromatic unknown
 58 | BAS                 | b | #### | basic unknown
 59 | HYP                 | # | #### | hydroxyproline
 60 | SAR                 | s | #### | sarcosine
 61 | FOR                 | f | #### | formyl
 62 | MSE                 | M | #### | selenomethionine
 63 | MEX                 | C | #### | cysteine bridged with beta-mercaptoethanol
 64 | SO4                 | # | SO4  | sulphate ion -2
 65 | ABU                 | # | #### | similar to Cys, but SG->CG
 66 | ACP                 | # | ACP  | acetylated N-terminus for proline
 67 | BRK                 | / | BRK  | chain break
 68 | HIS                 | H | HIS  | histidine for TOPH19
 69 | HIS                 | H | HSC  | doubly protonated HIS for TOPH19
 70 | PEN                 | # | PEN  | Penicillamine for TOPH19
 71 | FRM                 | # | FORM | for TOPH19
 72 | AMN                 | # | AMN  | for TOPH19
 73 | CBX                 | # | CBX  | for TOPH19
 74 | ETH                 | # | ETH  | for TOPH19
 75 | OHH                 | # | OH2  | TIPS3P water model for TOPH19
 76 | COH                 | # | COH  | for TOPH19
 77 | ST2                 | # | ST2  | for TOPH19
 78 | LTD                 | # | LTOD | patch for TOPH19
 79 | LG1                 | # | LIG1 | cyclic patch
 80 | LG2                 | # | LIG2 | cyclic patch
 81 | LG3                 | # | LIG3 | cyclic patch
 82 | BLK                 | . | BLK  | BLOCK, place holder
 83 | 5PH                 | # | 5PHO | 5'terminal PHOSPHATE patch
 84 | 3TE                 | # | 3TER | 3'terminal HYDROXYL patch, from MeOH
 85 | 3PH                 | # | 3PHO | 3'terminal PHOSPHATE patch
 86 | 9MG                 | # | 9MG  | 9-Methyl guanine patch
 87 | 9EG                 | # | 9EG  | 9-Ethyl guanine patch
 88 | 9MA                 | # | 9MA  | 9-Methyl adenine patch
 89 | 1MC                 | # | 1MC  | 1-Methyl Cytosine patch
 90 | 1MT                 | # | 1MT  | 1-Methyl Thymine patch
 91 | NAG                 | 1 | NAG  | N-ACETYL-D-GLUCOSAMINE
 92 | MAN                 | 2 | MAN  | ALPHA-D-MANNOSE
 93 | MN                  | 4 | MN   | manganese ion, +2
 94 | MYR                 | 5 | MYR  | MYRISTATE
 95 | GDP                 | x | GDP  | GDP
 96 | GTP                 | y | GTP  | GTP
 97 | LN2                 | # | LNK2 | NH3 Lys - CONH Gln (sc to sc) link patch
 98 | LN3                 | # | LNK3 | CO to NH3 Lys (backb to sdch) link patch
 99 | LN4                 | # | LNK4 | COOH to NH sdch to backb link patch
100 | IGL                 | q | IGLN | iso-glutamin
101 | 156                 | i | 0156 | 0156
102 | ATP                 | @ | ATP  | ATP
103 | MG                  | $ | MG   | magnesium ion
104 | K                   | % | K    | potassium ion
105 | 25P                 | # | 25P1 | patch to convert a 3'-5' phosphodiester
106 | 25P                 | # | 25P2 | patch to convert a 3'-5' phosphodiester
107 | 5DP                 | # | 5DP  | patch to create 5' diphosphate on nucleotides, jjp1/adm jr.
108 | 5MC                 | # | 5MC1 | Patch to generate 5-methylcytosine (base only)
109 | 5MC                 | # | 5MC2 | Patch to convert cytosine to 5-methylcytosine
110 | 5ME                 | # | 5MET | 5'-ribose METHYL patch
111 | 5TE                 | # | 5TER | 5'-terminal HYDROXYL patch, from MeOH
112 | ADE                 | # | ADE  |
113 | ADP                 | # | ADP  | adenosine diphosphate, jjp1/adm jr.
114 | CYT                 | # | CYT  |
115 | DEO                 | # | DEO1 | Patch to make DEOXYribose in PYRIMIDINES
116 | DEO                 | # | DEO2 | Patch to make DEOXYribose in PURINES
117 | DEO                 | # | DEOT | DEOXYRIBOSE, Wilma Olsen's dihedral model
118 | DMP                 | # | DMPA | Dimethylphosphate
119 | DUM                 | # | DUM  | DUMMY ATOM
120 | GUA                 | # | GUA  |
121 | INO                 | # | INO1 | patch to convert guanine to inosine
122 | MP_                 | # | MP_0 | Methylphosphate, neutral
123 | MP_                 | # | MP_1 | Methylphosphate, anionic
124 | MP_                 | # | MP_2 | Methylphosphate, dianionic
125 | NAD                 | # | NAD  | oxidized nicotinamide adenine dinucleotide, jjp1/adm jr.
126 | NAD                 | # | NADH | reduced nicotinamide adenine dinucleotide, jjp1/adm jr.
127 | NIC                 | # | NIC  | oxidized nicotinamide, jjp1/adm jr.
128 | NIC                 | # | NICH | reduced nicotinamide, jjp1/adm jr.
129 | PPI                 | # | PPI1 | Inorganic phosphate, jjp1/adm jr.
130 | PUR                 | # | PURA | Patch to generate ADENINE (purine)
131 | PUR                 | # | PURG | Patch to generate GUANINE (purine)
132 | PYR                 | # | PYRC | Patch to generate CYTOSINE (pyrimidine)
133 | PYR                 | # | PYRU | Patch to generate URACIL or THYMINE (pyrimidine)
134 | RIB                 | # | RIBT | RIBOSE, Wilma Olsen's dihedral model
135 | SOD                 | # | SOD  | Sodium Ion
136 | THY                 | # | THY  |
137 | TP1                 | # | TP1  | convert tyrosine to monoanionic phosphotyrosine
138 | TP1                 | # | TP1A | patch to convert tyrosine to
139 | TP2                 | # | TP2  | patch to convert tyrosine to
140 | TP2                 | # | TP2A | patch to convert tyrosine to
141 | URA                 | # | URA  |

iii) edit the template.pdb like

TER
ATOM   natom  MG  MG    nres      x   y  z

You can force the His to be in the same coordinate using:
 
 

http://salilab.org/modeller/manual/node68.html
 

Hope it helps
 

Luca

--------------------------------------------------------
Luca Settimo, Ph.D. Student
 

Molecular Structures and Biocomputing
Department of Biochemistry and Pharmacy
Åbo Akademi University
Tykistökatu 6A
20520 Turku Finland
phone: +358-2-215-4600
fax: +358-2-2153280
">mailto:
Webpage URL http://www.abo.fi/~lsettimo
--------------------------------------------------------