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Calcium in PDB 4b52: Crystal Structure of Gentlyase, the Neutral Metalloprotease of Paenibacillus Polymyxa

Enzymatic activity of Crystal Structure of Gentlyase, the Neutral Metalloprotease of Paenibacillus Polymyxa

All present enzymatic activity of Crystal Structure of Gentlyase, the Neutral Metalloprotease of Paenibacillus Polymyxa:
3.4.24.4;

Protein crystallography data

The structure of Crystal Structure of Gentlyase, the Neutral Metalloprotease of Paenibacillus Polymyxa, PDB code: 4b52 was solved by A.Ruf, M.Stihle, J.Benz, M.Schmidt, H.Sobek, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.60 / 1.76
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 61.121, 77.021, 64.443, 90.00, 103.58, 90.00
R / Rfree (%) 19.508 / 24.749

Other elements in 4b52:

The structure of Crystal Structure of Gentlyase, the Neutral Metalloprotease of Paenibacillus Polymyxa also contains other interesting chemical elements:

Zinc (Zn) 2 atoms
Sodium (Na) 1 atom

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Gentlyase, the Neutral Metalloprotease of Paenibacillus Polymyxa (pdb code 4b52). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 6 binding sites of Calcium where determined in the Crystal Structure of Gentlyase, the Neutral Metalloprotease of Paenibacillus Polymyxa, PDB code: 4b52:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in 4b52

Go back to Calcium Binding Sites List in 4b52
Calcium binding site 1 out of 6 in the Crystal Structure of Gentlyase, the Neutral Metalloprotease of Paenibacillus Polymyxa


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of Gentlyase, the Neutral Metalloprotease of Paenibacillus Polymyxa within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca402

b:14.2
occ:1.00
OD1 A:ASP129 2.3 12.9 1.0
OE1 A:GLN170 2.3 21.0 1.0
OD2 A:ASP131 2.3 16.3 1.0
O A:HOH2193 2.3 27.6 1.0
OD2 A:ASP129 2.3 15.0 1.0
OD1 A:ASP178 2.4 17.0 1.0
O A:HOH2170 2.5 19.1 1.0
CG A:ASP129 2.5 12.3 1.0
CG A:ASP131 3.2 14.7 1.0
OD2 A:ASP179 3.2 34.0 1.0
CD A:GLN170 3.4 27.0 1.0
CG A:ASP178 3.4 14.9 1.0
NE2 A:GLN170 3.8 26.0 1.0
OD2 A:ASP178 3.8 14.9 1.0
OD1 A:ASP131 3.9 16.6 1.0
CG A:ASP179 4.0 26.9 1.0
CB A:ASP131 4.1 13.2 1.0
CB A:ASP129 4.1 11.6 1.0
N A:ASP178 4.3 13.3 1.0
N A:ASP179 4.4 14.6 1.0
N A:GLY177 4.5 11.7 1.0
OD1 A:ASP179 4.5 25.8 1.0
O A:LEU175 4.5 14.2 1.0
N A:ASP131 4.6 12.1 1.0
CB A:ASP178 4.7 14.1 1.0
CG A:GLN170 4.8 30.1 1.0
O A:HOH2191 4.8 15.2 1.0
CB A:ASP179 4.9 19.2 1.0
CA A:ASP178 4.9 12.9 1.0
OD1 A:ASN173 4.9 14.2 1.0
CA A:ASP131 5.0 11.9 1.0
C A:GLY177 5.0 14.1 1.0
CD A:PRO130 5.0 11.2 1.0
CA A:ASP129 5.0 11.0 1.0

Calcium binding site 2 out of 6 in 4b52

Go back to Calcium Binding Sites List in 4b52
Calcium binding site 2 out of 6 in the Crystal Structure of Gentlyase, the Neutral Metalloprotease of Paenibacillus Polymyxa


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of Gentlyase, the Neutral Metalloprotease of Paenibacillus Polymyxa within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca403

b:12.7
occ:1.00
O A:HOH2101 2.3 15.5 1.0
O A:HOH2099 2.3 11.4 1.0
OD1 A:ASP53 2.3 11.4 1.0
OD1 A:ASP55 2.3 15.8 1.0
OD2 A:ASP53 2.3 14.2 1.0
O A:VAL57 2.4 14.6 1.0
CG A:ASP53 2.5 12.5 1.0
CG A:ASP55 3.3 15.3 1.0
C A:VAL57 3.5 16.0 1.0
OD2 A:ASP55 3.8 18.5 1.0
N A:VAL57 4.0 13.9 1.0
CB A:ASP53 4.1 12.2 1.0
N A:ASP55 4.2 13.6 1.0
CA A:VAL57 4.2 15.9 1.0
CB A:VAL57 4.4 18.3 1.0
O A:HOH2103 4.4 17.0 1.0
CB A:ASP55 4.5 14.7 1.0
O A:HOH2100 4.5 12.6 1.0
N A:TRP58 4.5 14.5 1.0
N A:ALA54 4.6 13.2 1.0
N A:ASN56 4.7 13.0 1.0
CA A:ASP55 4.7 15.0 1.0
CA A:TRP58 4.7 13.8 1.0
C A:ASP55 4.9 13.6 1.0
CA A:ASP53 4.9 12.1 1.0

Calcium binding site 3 out of 6 in 4b52

Go back to Calcium Binding Sites List in 4b52
Calcium binding site 3 out of 6 in the Crystal Structure of Gentlyase, the Neutral Metalloprotease of Paenibacillus Polymyxa


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of Gentlyase, the Neutral Metalloprotease of Paenibacillus Polymyxa within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca404

b:18.6
occ:1.00
O A:HOH2203 2.2 23.7 1.0
OD1 A:ASP188 2.3 17.7 1.0
O A:ILE185 2.3 24.9 1.0
O A:THR182 2.4 20.1 1.0
O A:HOH2201 2.4 17.1 1.0
OG1 A:THR182 2.4 21.1 1.0
O A:TYR181 2.4 17.4 1.0
C A:THR182 3.2 21.4 1.0
CG A:ASP188 3.4 15.7 1.0
C A:TYR181 3.4 16.6 1.0
C A:ILE185 3.5 26.6 1.0
CB A:THR182 3.6 20.2 1.0
CA A:THR182 3.8 20.2 1.0
OD2 A:ASP188 3.8 20.6 1.0
N A:THR182 4.0 18.1 1.0
N A:ILE185 4.2 28.4 1.0
CA A:ILE185 4.3 26.6 1.0
CB A:ILE185 4.3 26.0 1.0
N A:PRO183 4.3 25.4 1.0
N A:ALA186 4.5 26.0 1.0
CB A:TYR181 4.5 17.2 1.0
CA A:TYR181 4.6 16.4 1.0
O A:ASP188 4.6 16.3 1.0
N A:ASP188 4.6 19.8 1.0
CA A:ALA186 4.6 25.9 1.0
O A:ASP178 4.6 15.7 1.0
CD2 A:TYR181 4.7 16.7 1.0
CB A:ASP188 4.7 15.2 1.0
C A:ASP188 4.7 15.9 1.0
CA A:PRO183 4.7 27.5 1.0
CG2 A:THR182 4.8 20.1 1.0
C A:ALA186 4.9 25.8 1.0
CG2 A:ILE185 4.9 24.9 1.0
CA A:ASP188 4.9 17.5 1.0
C A:PRO183 4.9 29.0 1.0
CG A:TYR181 5.0 18.9 1.0

Calcium binding site 4 out of 6 in 4b52

Go back to Calcium Binding Sites List in 4b52
Calcium binding site 4 out of 6 in the Crystal Structure of Gentlyase, the Neutral Metalloprotease of Paenibacillus Polymyxa


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystal Structure of Gentlyase, the Neutral Metalloprotease of Paenibacillus Polymyxa within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca402

b:14.0
occ:1.00
OE1 B:GLN170 2.3 19.3 1.0
OD2 B:ASP131 2.3 15.8 1.0
OD2 B:ASP129 2.3 14.3 1.0
OD1 B:ASP129 2.3 11.0 1.0
OD1 B:ASP178 2.3 16.8 1.0
O B:HOH2179 2.5 25.5 1.0
CG B:ASP129 2.5 12.2 1.0
O B:HOH2155 2.7 16.6 1.0
CG B:ASP131 3.2 15.7 1.0
CD B:GLN170 3.3 26.5 1.0
CG B:ASP178 3.5 16.1 1.0
NE2 B:GLN170 3.7 27.1 1.0
OD2 B:ASP179 3.8 21.4 1.0
OD2 B:ASP178 3.9 16.8 1.0
OD1 B:ASP131 3.9 17.7 1.0
CG B:ASP179 4.1 20.3 1.0
CB B:ASP131 4.2 13.4 1.0
CB B:ASP129 4.2 10.6 1.0
OD1 B:ASP179 4.3 18.8 1.0
N B:ASP178 4.3 13.7 1.0
N B:GLY177 4.5 10.7 1.0
N B:ASP179 4.5 12.1 1.0
N B:ASP131 4.7 10.4 1.0
CG B:GLN170 4.7 31.0 1.0
O B:LEU175 4.7 10.3 1.0
O B:HOH2177 4.7 16.1 1.0
CB B:ASP178 4.7 15.1 1.0
CB B:ASP179 4.8 15.3 1.0
CD B:PRO130 4.9 10.2 1.0
CA B:ASP178 4.9 13.6 1.0
CA B:ASP129 5.0 10.7 1.0
CA B:ASP131 5.0 10.5 1.0

Calcium binding site 5 out of 6 in 4b52

Go back to Calcium Binding Sites List in 4b52
Calcium binding site 5 out of 6 in the Crystal Structure of Gentlyase, the Neutral Metalloprotease of Paenibacillus Polymyxa


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Crystal Structure of Gentlyase, the Neutral Metalloprotease of Paenibacillus Polymyxa within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca403

b:15.9
occ:1.00
O B:HOH2083 2.1 19.1 1.0
O B:HOH2088 2.3 18.6 1.0
OD1 B:ASP53 2.3 16.7 1.0
OD2 B:ASP53 2.3 16.0 1.0
O B:VAL57 2.3 12.8 1.0
OD1 B:ASP55 2.4 18.1 1.0
O B:HOH2084 2.4 14.0 1.0
CG B:ASP53 2.5 16.1 1.0
CG B:ASP55 3.4 19.4 1.0
C B:VAL57 3.5 13.3 1.0
OD2 B:ASP55 4.0 19.6 1.0
N B:VAL57 4.1 15.0 1.0
CB B:ASP53 4.1 15.1 1.0
CA B:VAL57 4.2 15.6 1.0
N B:ASP55 4.3 18.0 1.0
OD1 B:ASN59 4.3 26.6 1.0
O B:HOH2085 4.4 13.2 1.0
O B:HOH2092 4.4 25.1 1.0
CB B:VAL57 4.5 14.8 1.0
O B:HOH2082 4.5 19.1 1.0
N B:TRP58 4.5 12.3 1.0
CB B:ASP55 4.6 19.6 1.0
O B:HOH2041 4.6 30.7 1.0
N B:ASN56 4.6 17.6 1.0
CA B:TRP58 4.6 13.5 1.0
N B:ALA54 4.7 16.7 1.0
CA B:ASP55 4.8 17.3 1.0
O B:HOH2040 4.8 45.8 1.0
C B:ASP55 4.9 18.0 1.0
CA B:ASP53 5.0 14.3 1.0

Calcium binding site 6 out of 6 in 4b52

Go back to Calcium Binding Sites List in 4b52
Calcium binding site 6 out of 6 in the Crystal Structure of Gentlyase, the Neutral Metalloprotease of Paenibacillus Polymyxa


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Crystal Structure of Gentlyase, the Neutral Metalloprotease of Paenibacillus Polymyxa within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca404

b:15.2
occ:1.00
O B:HOH2187 2.2 15.4 1.0
O B:TYR181 2.3 13.7 1.0
O B:ILE185 2.3 20.8 1.0
OD1 B:ASP188 2.3 17.5 1.0
OG1 B:THR182 2.4 14.2 1.0
O B:HOH2191 2.4 19.9 1.0
O B:THR182 2.4 14.3 1.0
C B:THR182 3.2 14.7 1.0
C B:TYR181 3.3 13.2 1.0
CB B:THR182 3.4 15.2 1.0
CG B:ASP188 3.4 17.5 1.0
C B:ILE185 3.5 21.3 1.0
CA B:THR182 3.7 14.9 1.0
OD2 B:ASP188 3.8 16.9 1.0
N B:THR182 3.9 13.6 1.0
CA B:ILE185 4.2 18.8 1.0
N B:ILE185 4.2 20.0 1.0
N B:PRO183 4.3 16.8 1.0
CB B:ILE185 4.3 18.6 1.0
O B:ASP178 4.4 11.4 1.0
O B:HOH2189 4.4 24.6 1.0
O B:ASP188 4.5 17.5 1.0
O B:HOH2193 4.5 28.8 1.0
CA B:TYR181 4.5 11.4 1.0
O B:HOH2188 4.5 33.2 1.0
N B:ALA186 4.6 22.3 1.0
N B:ASP188 4.6 20.0 1.0
CB B:TYR181 4.6 11.8 1.0
C B:ASP188 4.7 16.2 1.0
CD2 B:TYR181 4.7 13.7 1.0
CB B:ASP188 4.7 17.7 1.0
CA B:ALA186 4.8 22.9 1.0
CG2 B:THR182 4.8 14.5 1.0
CA B:PRO183 4.8 18.2 1.0
N B:TYR181 4.9 11.2 1.0
CA B:ASP188 4.9 18.0 1.0
C B:PRO183 5.0 19.4 1.0

Reference:

A.Ruf, M.Stihle, J.Benz, M.Schmidt, H.Sobek. Structure of Gentlyase, the Neutral Metalloprotease of Paenibacillus Polymyxa Acta Crystallogr.,Sect.D V. 69 24 2013.
ISSN: ISSN 0907-4449
PubMed: 23275160
DOI: 10.1107/S0907444912041169
Page generated: Sat Dec 12 04:40:32 2020

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