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Calcium in PDB 5wpp: Crystal Structure HPIC1 W73M/K132M

Protein crystallography data

The structure of Crystal Structure HPIC1 W73M/K132M, PDB code: 5wpp was solved by S.A.Newmister, S.Li, M.Garcia-Borras, J.N.Sanders, S.Yang, A.N.Lowell, F.Yu, J.L.Smith, R.M.Williams, K.N.Houk, D.H.Sherman, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 39.30 / 1.70
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 44.920, 81.140, 131.680, 90.00, 90.00, 90.00
R / Rfree (%) 18.1 / 21.5

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure HPIC1 W73M/K132M (pdb code 5wpp). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 10 binding sites of Calcium where determined in the Crystal Structure HPIC1 W73M/K132M, PDB code: 5wpp:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Calcium binding site 1 out of 10 in 5wpp

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Calcium binding site 1 out of 10 in the Crystal Structure HPIC1 W73M/K132M


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Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure HPIC1 W73M/K132M within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca301

b:23.1
occ:1.00
 OE2 A:GLU95 2.3 27.2 1.0
O A:GLY37 2.3 22.6 1.0
O A:GLU95 2.4 26.7 1.0
O A:ASN98 2.4 24.6 1.0
OE1 A:GLU39 2.4 22.0 1.0
OD1 A:ASP216 2.4 22.1 1.0
OD2 A:ASP216 2.9 26.9 1.0
CG A:ASP216 3.0 24.3 1.0
C A:GLU95 3.4 26.2 1.0
C A:GLY37 3.4 22.7 1.0
CD A:GLU95 3.5 33.4 1.0
C A:ASN98 3.5 24.6 1.0
CD A:GLU39 3.5 27.6 1.0
CA A:GLY37 3.8 22.0 1.0
N A:ASN98 3.9 25.4 1.0
CB A:GLU95 3.9 27.0 1.0
CG A:GLU39 4.1 26.0 1.0
CA A:GLU95 4.1 26.0 1.0
CA A:ASN98 4.2 20.7 1.0
N A:GLY96 4.3 27.1 1.0
CG A:GLU95 4.3 27.5 1.0
OE1 A:GLU95 4.3 35.3 1.0
N A:GLU95 4.4 27.7 1.0
CA A:GLY96 4.4 27.4 1.0
CB A:ASP216 4.5 22.3 1.0
OE2 A:GLU39 4.5 25.1 1.0
N A:ILE99 4.5 23.4 1.0
C A:GLY96 4.6 25.4 1.0
N A:PHE38 4.6 22.3 1.0
CB A:ASN98 4.6 20.7 1.0
N A:ARG97 4.6 25.8 1.0
CB A:ALA93 4.8 27.9 1.0
CA A:ILE99 4.8 22.9 1.0
N A:ASN217 4.8 23.4 1.0
N A:GLU39 4.9 23.2 1.0
C A:ARG97 4.9 23.6 1.0
C A:PHE38 4.9 22.9 1.0

Calcium binding site 2 out of 10 in 5wpp

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Calcium binding site 2 out of 10 in the Crystal Structure HPIC1 W73M/K132M


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Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure HPIC1 W73M/K132M within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca302

b:39.3
occ:1.00
 O A:GLU68 2.3 31.4 1.0
O A:HOH551 2.5 35.0 1.0
O A:HOH469 2.6 39.5 1.0
O A:HOH413 2.7 33.6 1.0
C A:GLU68 3.5 30.5 1.0
CA A:GLU68 4.1 33.3 1.0
O A:HOH428 4.3 35.9 1.0
CG A:ARG70 4.4 29.0 1.0
NE A:ARG70 4.5 29.6 1.0
O A:HOH524 4.5 38.4 1.0
O A:PRO67 4.5 27.4 1.0
N A:LYS69 4.6 30.0 1.0
N A:ARG70 4.7 26.8 1.0
O A:HOH505 4.7 31.5 1.0
CD A:ARG70 4.8 30.2 1.0
CA A:LYS69 4.8 30.1 1.0
CB A:GLU68 4.9 33.9 1.0

Calcium binding site 3 out of 10 in 5wpp

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Calcium binding site 3 out of 10 in the Crystal Structure HPIC1 W73M/K132M


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Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure HPIC1 W73M/K132M within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca303

b:40.0
occ:1.00
 O A:PHE178 2.4 27.1 1.0
O A:HOH577 2.5 42.1 1.0
O A:HOH421 2.5 29.9 1.0
O A:HOH448 2.5 40.9 1.0
O A:HOH555 2.5 42.5 1.0
O A:HOH568 2.6 42.6 1.0
O A:HOH553 2.6 41.7 1.0
C A:PHE178 3.6 26.6 1.0
OE1 A:GLN91 4.2 36.6 1.0
N A:PHE178 4.2 25.7 1.0
CG A:LYS179 4.4 28.3 1.0
CA A:PHE178 4.5 26.9 1.0
N A:LYS179 4.5 24.7 1.0
CA A:LYS179 4.6 25.2 1.0
OE2 A:GLU177 4.8 39.2 1.0
CB A:PHE178 4.9 26.7 1.0
CB A:GLU177 4.9 31.6 1.0

Calcium binding site 4 out of 10 in 5wpp

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Calcium binding site 4 out of 10 in the Crystal Structure HPIC1 W73M/K132M


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystal Structure HPIC1 W73M/K132M within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca304

b:27.4
occ:1.00
 O A:GLY149 2.3 26.8 1.0
OD1 A:ASN137 2.3 26.6 1.0
O A:PHE138 2.3 30.7 1.0
OD1 A:ASP175 2.3 31.0 1.0
O A:LEU147 2.3 28.9 1.0
O A:HOH453 2.4 28.4 1.0
CG A:ASN137 3.4 27.1 1.0
C A:GLY149 3.4 26.9 1.0
C A:PHE138 3.4 28.8 1.0
C A:LEU147 3.5 32.5 1.0
CG A:ASP175 3.6 30.0 1.0
N A:GLY149 3.7 30.1 1.0
C A:ALA148 3.8 31.2 1.0
ND2 A:ASN137 3.9 27.6 1.0
N A:PHE138 3.9 26.8 1.0
CA A:ALA148 4.0 33.8 1.0
CA A:PHE138 4.1 29.4 1.0
CA A:GLY149 4.2 28.3 1.0
N A:ALA148 4.2 32.0 1.0
C A:ASN137 4.3 27.1 1.0
CB A:PHE138 4.3 31.4 1.0
OD2 A:ASP175 4.4 35.1 1.0
O A:ALA148 4.4 27.8 1.0
O A:PHE210 4.5 27.5 1.0
CB A:ASP175 4.5 28.3 1.0
N A:PHE150 4.5 27.1 1.0
N A:GLY139 4.5 28.5 1.0
CB A:LEU147 4.6 31.4 1.0
CB A:ASN137 4.6 27.6 1.0
O A:HOH506 4.6 34.6 1.0
CA A:LEU147 4.6 33.6 1.0
CA A:ASP175 4.7 27.6 1.0
O A:ASN137 4.7 28.0 1.0
CA A:GLY139 4.7 25.9 1.0
CB A:PHE210 4.7 29.0 1.0
CA A:ASN137 4.7 26.1 1.0
CA A:PHE150 4.8 29.5 1.0
CD2 A:PHE210 4.8 29.1 1.0
O A:GLY212 4.8 26.4 1.0

Calcium binding site 5 out of 10 in 5wpp

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Calcium binding site 5 out of 10 in the Crystal Structure HPIC1 W73M/K132M


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Crystal Structure HPIC1 W73M/K132M within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca305

b:32.1
occ:0.47
 O A:TYR49 2.2 30.3 1.0
O A:HOH497 2.3 37.1 0.7
O A:HOH521 2.3 39.4 1.0
OD1 A:ASP48 2.5 31.2 1.0
O A:HOH527 2.8 38.5 1.0
C A:TYR49 3.4 29.2 1.0
CG A:ASP48 3.6 29.3 1.0
N A:TYR49 3.7 27.7 1.0
CA A:TYR49 4.1 25.0 1.0
OD2 A:ASP48 4.1 29.6 1.0
N A:THR50 4.4 25.8 1.0
C A:ASP48 4.6 27.0 1.0
CA A:THR50 4.6 24.0 1.0
CA A:ASP48 4.8 27.6 1.0
CB A:ASP48 4.8 27.8 1.0
O A:HOH485 4.9 29.3 1.0
CB A:TYR49 5.0 27.1 1.0

Calcium binding site 6 out of 10 in 5wpp

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Calcium binding site 6 out of 10 in the Crystal Structure HPIC1 W73M/K132M


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Crystal Structure HPIC1 W73M/K132M within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca301

b:19.5
occ:1.00
 O B:ASN98 2.3 20.9 1.0
O B:GLU95 2.3 21.2 1.0
OE2 B:GLU95 2.3 22.5 1.0
O B:GLY37 2.3 20.8 1.0
OE2 B:GLU39 2.4 19.1 1.0
OD1 B:ASP216 2.4 19.5 1.0
OD2 B:ASP216 2.9 24.6 1.0
CG B:ASP216 3.0 21.6 1.0
C B:GLU95 3.3 21.4 1.0
C B:GLY37 3.4 20.3 1.0
C B:ASN98 3.5 20.6 1.0
CD B:GLU39 3.5 22.8 1.0
CD B:GLU95 3.5 25.4 1.0
CA B:GLY37 3.8 18.8 1.0
N B:ASN98 3.9 19.8 1.0
CB B:GLU95 3.9 21.9 1.0
CG B:GLU39 4.1 21.6 1.0
CA B:GLU95 4.1 19.6 1.0
CA B:ASN98 4.2 19.1 1.0
N B:GLY96 4.3 22.3 1.0
CG B:GLU95 4.3 24.6 1.0
OE1 B:GLU95 4.3 31.3 1.0
CA B:GLY96 4.4 22.2 1.0
N B:GLU95 4.4 19.5 1.0
CB B:ASP216 4.5 21.1 1.0
OE1 B:GLU39 4.5 23.6 1.0
N B:ILE99 4.5 19.0 1.0
C B:GLY96 4.6 22.6 1.0
N B:PHE38 4.6 19.0 1.0
CB B:ASN98 4.6 18.0 1.0
N B:ARG97 4.7 22.5 1.0
CB B:ALA93 4.8 20.5 1.0
CA B:ILE99 4.8 19.0 1.0
N B:ASN217 4.8 21.4 1.0
N B:GLU39 4.9 19.8 1.0
C B:PHE38 4.9 20.4 1.0
C B:ARG97 4.9 20.4 1.0

Calcium binding site 7 out of 10 in 5wpp

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Calcium binding site 7 out of 10 in the Crystal Structure HPIC1 W73M/K132M


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Crystal Structure HPIC1 W73M/K132M within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca302

b:32.0
occ:1.00
 O B:HOH574 2.3 38.3 1.0
O B:PHE178 2.4 21.7 1.0
O B:HOH486 2.4 27.6 1.0
O B:HOH634 2.4 35.5 1.0
O B:HOH597 2.5 34.4 1.0
O B:HOH610 2.5 38.0 1.0
O B:HOH425 2.8 26.5 1.0
C B:PHE178 3.6 21.9 1.0
OE1 B:GLN91 4.2 25.7 1.0
N B:PHE178 4.2 19.2 1.0
CG B:LYS179 4.4 22.8 1.0
CA B:PHE178 4.4 18.9 1.0
N B:LYS179 4.5 21.0 1.0
CA B:LYS179 4.6 19.8 1.0
O B:HOH602 4.6 36.5 1.0
OE1 B:GLU177 4.7 38.0 1.0
O B:HOH589 4.8 34.8 1.0
CB B:PHE178 4.9 22.3 1.0
O B:HOH582 4.9 29.7 1.0

Calcium binding site 8 out of 10 in 5wpp

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Calcium binding site 8 out of 10 in the Crystal Structure HPIC1 W73M/K132M


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Crystal Structure HPIC1 W73M/K132M within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca303

b:24.1
occ:1.00
 O B:PHE138 2.2 28.4 1.0
OD1 B:ASN137 2.3 23.5 1.0
OD1 B:ASP175 2.3 26.5 1.0
O B:GLY149 2.3 25.0 1.0
O B:LEU147 2.4 25.0 1.0
O B:HOH474 2.4 26.1 1.0
CG B:ASN137 3.3 21.3 1.0
C B:PHE138 3.4 27.2 1.0
C B:GLY149 3.5 24.6 1.0
CG B:ASP175 3.5 27.8 1.0
C B:LEU147 3.6 30.4 1.0
N B:GLY149 3.7 26.6 1.0
ND2 B:ASN137 3.8 22.6 1.0
C B:ALA148 3.8 27.4 1.0
N B:PHE138 4.0 23.1 1.0
CA B:ALA148 4.1 29.3 1.0
CA B:PHE138 4.1 27.0 1.0
CA B:GLY149 4.2 26.0 1.0
C B:ASN137 4.3 23.0 1.0
N B:ALA148 4.3 29.7 1.0
OD2 B:ASP175 4.3 33.0 1.0
CB B:PHE138 4.3 29.5 1.0
O B:ALA148 4.4 29.1 1.0
CB B:ASP175 4.5 29.8 1.0
N B:GLY139 4.5 24.9 1.0
N B:PHE150 4.5 26.7 1.0
O B:HOH533 4.5 27.3 1.0
O B:PHE210 4.5 26.0 1.0
CB B:ASN137 4.6 22.4 1.0
O B:ASN137 4.6 24.3 1.0
CB B:LEU147 4.6 28.5 1.0
CA B:GLY139 4.7 25.2 1.0
CA B:LEU147 4.7 30.8 1.0
CA B:ASP175 4.7 24.8 1.0
CD2 B:PHE210 4.7 27.2 1.0
CA B:ASN137 4.8 22.5 1.0
CB B:PHE210 4.8 27.5 1.0
CA B:PHE150 4.8 26.8 1.0
O B:GLY212 4.9 25.6 1.0

Calcium binding site 9 out of 10 in 5wpp

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Calcium binding site 9 out of 10 in the Crystal Structure HPIC1 W73M/K132M


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 9 of Crystal Structure HPIC1 W73M/K132M within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca304

b:62.0
occ:1.00
 O B:HOH457 2.6 42.7 1.0
O B:HOH637 2.6 53.2 1.0
OD1 B:ASP161 2.6 41.7 1.0
O B:HOH502 2.6 39.0 1.0
O B:HOH596 2.9 43.5 1.0
CG B:ASP161 3.7 39.8 1.0
OD2 B:ASP161 4.2 46.3 1.0
OE2 B:GLU116 4.4 34.7 1.0
O B:HOH414 4.4 45.5 1.0
OE1 B:GLU116 4.5 36.4 1.0
NH2 B:ARG201 4.5 30.9 1.0
CB B:ASP161 4.8 33.4 1.0
CD B:GLU116 4.9 35.4 1.0

Calcium binding site 10 out of 10 in 5wpp

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Calcium binding site 10 out of 10 in the Crystal Structure HPIC1 W73M/K132M


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 10 of Crystal Structure HPIC1 W73M/K132M within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca305

b:29.6
occ:0.56
 O B:TYR49 2.3 28.2 1.0
OD1 B:ASP48 2.5 35.1 1.0
O B:HOH550 2.5 35.3 0.8
O B:HOH469 3.1 39.1 1.0
C B:TYR49 3.4 27.0 1.0
CG B:ASP48 3.5 31.0 1.0
N B:TYR49 3.7 24.8 1.0
OD2 B:ASP48 3.9 34.2 1.0
CA B:TYR49 4.2 25.1 1.0
N B:THR50 4.4 23.8 1.0
CA B:THR50 4.6 25.5 1.0
C B:ASP48 4.6 27.6 1.0
CB B:ASP48 4.7 28.6 1.0
CA B:ASP48 4.8 23.5 1.0

Reference:

S.A.Newmister, S.Li, M.Garcia-Borras, J.N.Sanders, S.Yang, A.N.Lowell, F.Yu, J.L.Smith, R.M.Williams, K.N.Houk, D.H.Sherman. Structural Basis of the Cope Rearrangement and Cyclization in Hapalindole Biogenesis. Nat. Chem. Biol. V. 14 345 2018.
ISSN: ESSN 1552-4469
PubMed: 29531360
DOI: 10.1038/S41589-018-0003-X
Page generated: Mon Jul 15 13:22:19 2024

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