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Calcium in PDB 3lun: Structure of Ulilysin Mutant M290C

Protein crystallography data

The structure of Structure of Ulilysin Mutant M290C, PDB code: 3lun was solved by C.Tallant, R.Garcia-Castellanos, U.Baumann, F.X.Gomis-Ruth, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 39.93 / 1.80
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 58.510, 116.290, 164.760, 90.00, 90.00, 90.00
R / Rfree (%) 16.1 / 20.8

Other elements in 3lun:

The structure of Structure of Ulilysin Mutant M290C also contains other interesting chemical elements:

Zinc (Zn) 2 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Structure of Ulilysin Mutant M290C (pdb code 3lun). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 6 binding sites of Calcium where determined in the Structure of Ulilysin Mutant M290C, PDB code: 3lun:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in 3lun

Go back to Calcium Binding Sites List in 3lun
Calcium binding site 1 out of 6 in the Structure of Ulilysin Mutant M290C


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Structure of Ulilysin Mutant M290C within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1400

b:15.9
occ:1.00
 OD2 B:ASP152 2.2 13.7 1.0
O A:HOH561 2.3 26.4 1.0
O A:HOH484 2.3 22.3 1.0
OD2 A:ASP152 2.3 14.2 1.0
O A:HOH8 2.4 17.1 1.0
O B:HOH447 2.4 23.4 1.0
CG B:ASP152 3.4 15.3 1.0
CG A:ASP152 3.4 15.2 1.0
CB B:ASP152 4.0 14.2 1.0
O B:HOH385 4.1 17.1 1.0
CB A:ASP152 4.1 12.6 1.0
O A:HOH343 4.1 17.4 1.0
O B:SER151 4.1 14.5 1.0
O A:SER151 4.1 14.9 1.0
OD1 B:ASP152 4.3 14.6 1.0
OD1 A:ASP152 4.4 15.4 1.0
O A:HOH452 4.4 32.9 1.0
C B:SER151 4.5 14.5 1.0
CG2 B:THR200 4.6 14.5 1.0
C A:SER151 4.6 14.5 1.0
OG1 A:THR200 4.6 14.8 1.0
O A:THR150 4.6 15.9 1.0
OG1 B:THR200 4.6 13.9 1.0
O B:THR150 4.7 15.6 1.0
CG2 A:THR200 4.7 14.4 1.0
CB B:THR200 4.8 13.5 1.0
O A:HOH392 4.8 31.0 1.0
CB A:THR200 4.9 15.2 1.0
CA B:SER151 5.0 15.5 1.0

Calcium binding site 2 out of 6 in 3lun

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Calcium binding site 2 out of 6 in the Structure of Ulilysin Mutant M290C


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Structure of Ulilysin Mutant M290C within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca998

b:15.9
occ:1.00
 OD1 A:ASP254 2.3 16.0 1.0
O A:VAL256 2.3 16.6 1.0
O A:HOH354 2.3 15.0 1.0
O A:HOH12 2.4 15.5 1.0
O A:THR259 2.4 15.4 1.0
O A:HOH13 2.4 18.6 1.0
O A:HOH450 2.5 27.2 1.0
OG1 A:THR259 2.5 15.1 1.0
CG A:ASP254 3.2 18.2 1.0
C A:THR259 3.4 15.1 1.0
C A:VAL256 3.4 17.0 1.0
CB A:THR259 3.6 15.3 1.0
OD2 A:ASP254 3.7 16.7 1.0
N A:VAL256 3.9 19.0 1.0
CA A:THR259 3.9 16.0 1.0
CA A:VAL256 4.1 17.2 1.0
N A:THR259 4.1 16.3 1.0
O A:PRO260 4.2 16.6 1.0
N A:ASP254 4.3 20.4 1.0
C A:PRO260 4.3 16.5 1.0
O A:HOH421 4.4 28.9 1.0
CB A:VAL256 4.4 17.1 1.0
CB A:ASP254 4.5 18.5 1.0
N A:ASP257 4.5 17.4 1.0
N A:PRO260 4.5 15.7 1.0
N A:ASN261 4.5 17.7 1.0
O A:HOH498 4.6 40.4 1.0
O A:ASP257 4.6 18.6 1.0
O A:HOH359 4.6 18.1 1.0
O A:HOH336 4.6 34.4 1.0
C A:ASP257 4.6 17.7 1.0
OG A:SER253 4.7 21.4 1.0
CA A:ASP257 4.7 18.3 1.0
O A:ILE239 4.7 16.0 1.0
CA A:ASP254 4.8 18.7 1.0
N A:GLU255 4.8 19.1 1.0
CG2 A:THR259 4.9 15.3 1.0
CA A:PRO260 4.9 16.0 1.0
CA A:ASN261 4.9 17.0 1.0
C A:ASP254 4.9 19.1 1.0

Calcium binding site 3 out of 6 in 3lun

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Calcium binding site 3 out of 6 in the Structure of Ulilysin Mutant M290C


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Structure of Ulilysin Mutant M290C within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca997

b:15.7
occ:1.00
 O A:TRP240 2.1 14.4 1.0
O A:PRO249 2.2 21.9 1.0
O A:HOH485 2.2 18.5 1.0
O A:GLN262 2.3 14.6 1.0
O A:ALA263 2.3 15.4 1.0
OE1 A:GLU243 2.4 16.8 1.0
OE2 A:GLU243 2.4 17.7 1.0
CD A:GLU243 2.6 15.3 1.0
C A:ALA263 3.2 16.0 1.0
C A:TRP240 3.3 14.5 1.0
C A:PRO249 3.4 22.4 1.0
C A:GLN262 3.4 14.4 1.0
CA A:ALA263 3.5 16.1 1.0
N A:ALA263 3.9 14.9 1.0
CA A:TRP240 4.0 14.0 1.0
CB A:TRP240 4.1 14.4 1.0
CG A:GLU243 4.1 17.0 1.0
O A:ARG252 4.2 22.5 1.0
O A:HOH18 4.2 19.2 1.0
N A:CYS250 4.2 21.9 1.0
O A:HOH359 4.3 18.1 1.0
CA A:CYS250 4.3 22.9 1.0
CA A:PRO249 4.3 22.6 1.0
N A:ASP264 4.4 15.8 1.0
N A:GLY241 4.4 14.4 1.0
CD1 A:TRP240 4.6 15.3 1.0
CA A:GLY241 4.6 15.5 1.0
N A:ARG252 4.7 23.0 1.0
CA A:GLN262 4.7 14.2 1.0
OD1 A:ASN261 4.7 19.2 1.0
C A:CYS250 4.7 22.6 1.0
N A:GLN262 4.8 15.5 1.0
CG A:TRP240 4.8 13.8 1.0
N A:SER251 4.8 22.9 1.0
CB A:GLU243 4.9 16.9 1.0
CB A:PRO249 4.9 22.4 1.0
SG A:CYS277 4.9 23.7 1.0
CB A:ALA263 4.9 17.2 1.0

Calcium binding site 4 out of 6 in 3lun

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Calcium binding site 4 out of 6 in the Structure of Ulilysin Mutant M290C


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Structure of Ulilysin Mutant M290C within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca1401

b:36.0
occ:1.00
 O A:HOH507 2.3 33.3 1.0
O B:HOH504 2.4 25.1 1.0
O A:HOH506 2.4 25.3 1.0
O B:PRO194 2.5 19.0 1.0
O B:HOH505 2.5 21.7 1.0
C B:PRO194 3.6 18.9 1.0
C B:GLY195 3.8 22.5 1.0
N B:GLY196 3.9 21.8 1.0
CA B:GLY195 3.9 21.5 1.0
OE2 A:GLU153 4.0 23.2 1.0
O B:PHE193 4.1 15.8 1.0
N B:GLY195 4.2 19.6 1.0
O B:GLY195 4.3 24.1 1.0
O B:HOH390 4.4 26.5 1.0
OG1 A:THR149 4.4 16.6 1.0
C B:PHE193 4.4 16.5 1.0
OG A:SER151 4.4 19.6 1.0
OE1 A:GLU182 4.5 36.9 1.0
CB B:PHE193 4.5 16.8 1.0
CA B:GLY196 4.5 18.1 1.0
O A:HOH570 4.5 34.7 1.0
O B:HOH352 4.7 32.4 1.0
CG2 A:THR149 4.7 17.0 1.0
N B:PRO194 4.7 17.1 1.0
CA B:PRO194 4.8 17.6 1.0
CB A:SER151 4.8 15.8 1.0
O B:HOH355 4.8 27.6 1.0

Calcium binding site 5 out of 6 in 3lun

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Calcium binding site 5 out of 6 in the Structure of Ulilysin Mutant M290C


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Structure of Ulilysin Mutant M290C within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca998

b:13.8
occ:1.00
 O B:HOH559 2.3 16.4 1.0
O B:VAL256 2.3 15.8 1.0
OD2 B:ASP254 2.3 14.1 1.0
O B:THR259 2.4 14.1 1.0
O B:HOH2 2.5 13.4 1.0
O B:HOH1 2.5 19.4 1.0
OG1 B:THR259 2.5 12.6 1.0
O B:HOH428 2.5 26.7 1.0
CG B:ASP254 3.3 16.4 1.0
C B:THR259 3.4 14.2 1.0
C B:VAL256 3.5 16.8 1.0
CB B:THR259 3.6 13.4 1.0
OD1 B:ASP254 3.7 16.2 1.0
CA B:THR259 3.9 14.0 1.0
N B:VAL256 4.0 17.4 1.0
N B:THR259 4.0 13.8 1.0
CA B:VAL256 4.2 16.4 1.0
O B:PRO260 4.3 15.3 1.0
C B:PRO260 4.3 15.3 1.0
CB B:VAL256 4.4 16.0 1.0
N B:ASP254 4.4 17.0 1.0
N B:ASN261 4.5 16.1 1.0
N B:PRO260 4.5 14.2 1.0
O B:ASP257 4.5 17.9 1.0
N B:ASP257 4.6 16.8 1.0
CB B:ASP254 4.6 15.3 1.0
O B:HOH512 4.6 25.0 1.0
C B:ASP257 4.6 17.1 1.0
O B:HOH3 4.7 13.6 1.0
O B:HOH476 4.7 28.5 1.0
OG B:SER253 4.7 16.1 1.0
O B:ILE239 4.7 14.5 1.0
CA B:ASP257 4.8 17.8 1.0
CA B:ASN261 4.8 16.6 1.0
N B:GLU255 4.8 18.2 1.0
CA B:PRO260 4.9 15.2 1.0
CG2 B:THR259 4.9 12.6 1.0
O B:HOH536 4.9 42.7 1.0
CA B:ASP254 4.9 16.1 1.0

Calcium binding site 6 out of 6 in 3lun

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Calcium binding site 6 out of 6 in the Structure of Ulilysin Mutant M290C


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Structure of Ulilysin Mutant M290C within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca997

b:14.2
occ:1.00
 O B:TRP240 2.1 12.8 1.0
O B:PRO249 2.2 19.1 1.0
O B:HOH560 2.2 16.3 1.0
O B:GLN262 2.3 13.7 1.0
OE1 B:GLU243 2.4 16.4 1.0
O B:ALA263 2.4 14.1 1.0
OE2 B:GLU243 2.4 13.9 1.0
CD B:GLU243 2.7 16.3 1.0
C B:ALA263 3.3 13.1 1.0
C B:TRP240 3.3 12.6 1.0
C B:PRO249 3.4 19.2 1.0
C B:GLN262 3.4 14.7 1.0
CA B:ALA263 3.5 14.2 1.0
N B:ALA263 3.9 14.4 1.0
CA B:TRP240 4.0 13.1 1.0
CB B:TRP240 4.1 12.2 1.0
CG B:GLU243 4.2 13.4 1.0
O B:HOH5 4.2 18.1 1.0
O B:HOH3 4.2 13.6 1.0
O B:ARG252 4.2 18.1 1.0
CA B:PRO249 4.3 19.5 1.0
N B:CYS250 4.3 19.7 1.0
CA B:CYS250 4.3 20.7 1.0
N B:GLY241 4.3 12.3 1.0
N B:ASP264 4.5 13.5 1.0
CA B:GLY241 4.6 14.3 1.0
CD1 B:TRP240 4.6 14.1 1.0
CA B:GLN262 4.7 14.6 1.0
C B:CYS250 4.7 20.0 1.0
OD1 B:ASN261 4.7 20.1 1.0
N B:ARG252 4.7 17.6 1.0
N B:GLN262 4.8 14.8 1.0
N B:SER251 4.8 20.5 1.0
CG B:TRP240 4.8 13.9 1.0
CB B:PRO249 4.8 19.8 1.0
SG B:CYS277 4.9 22.6 1.0
CB B:ALA263 4.9 14.4 1.0
C B:GLY241 5.0 14.5 1.0

Reference:

C.Tallant, R.Garcia-Castellanos, U.Baumann, F.X.Gomis-Ruth. On the Relevance of the Met-Turn Methionine in Metzincins. J.Biol.Chem. V. 285 13951 2010.
ISSN: ISSN 0021-9258
PubMed: 20202937
DOI: 10.1074/JBC.M109.083378
Page generated: Sat Jul 13 13:17:57 2024

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