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Calcium in PDB 3mmz: Crystal Structure of Putative Had Family Hydrolase From Streptomyces Avermitilis Ma-4680

Protein crystallography data

The structure of Crystal Structure of Putative Had Family Hydrolase From Streptomyces Avermitilis Ma-4680, PDB code: 3mmz was solved by V.N.Malashkevich, U.A.Ramagopal, R.Toro, J.M.Sauder, S.K.Burley, S.C.Almo, New York Sgx Research Center For Structural Genomics (Nysgxrc), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.75 / 1.84
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 100.387, 115.723, 115.192, 90.00, 90.00, 90.00
R / Rfree (%) 17.5 / 20.9

Other elements in 3mmz:

The structure of Crystal Structure of Putative Had Family Hydrolase From Streptomyces Avermitilis Ma-4680 also contains other interesting chemical elements:

Chlorine (Cl) 4 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Putative Had Family Hydrolase From Streptomyces Avermitilis Ma-4680 (pdb code 3mmz). 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 Putative Had Family Hydrolase From Streptomyces Avermitilis Ma-4680, PDB code: 3mmz:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in 3mmz

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Calcium binding site 1 out of 6 in the Crystal Structure of Putative Had Family Hydrolase From Streptomyces Avermitilis Ma-4680


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 Putative Had Family Hydrolase From Streptomyces Avermitilis Ma-4680 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca500

b:10.3
occ:1.00
 O A:ASP20 2.3 10.1 1.0
OD2 A:ASP18 2.3 14.9 1.0
O A:HOH224 2.3 18.1 1.0
OD1 A:ASN110 2.3 11.9 1.0
O A:HOH187 2.3 19.9 1.0
O A:HOH200 2.5 18.3 1.0
CG A:ASP18 3.2 13.7 1.0
OD1 A:ASP18 3.4 14.1 1.0
CG A:ASN110 3.4 9.8 1.0
C A:ASP20 3.5 10.3 1.0
ND2 A:ASN110 3.9 11.1 1.0
OD2 A:ASP114 4.2 13.8 1.0
CA A:ASP20 4.3 10.6 1.0
N A:ASP20 4.4 9.7 1.0
N A:GLY21 4.5 9.5 1.0
CB A:ASP20 4.5 12.0 1.0
OD1 A:ASP26 4.5 13.5 1.0
CA A:GLY21 4.5 9.1 1.0
OG1 A:THR22 4.6 12.5 1.0
O A:HOH375 4.6 34.4 1.0
CB A:ASP18 4.6 13.1 1.0
OD1 A:ASN113 4.7 20.0 1.0
CB A:ASN110 4.7 11.0 1.0
O A:HOH469 4.7 42.6 1.0
ND2 A:ASN113 4.9 20.5 1.0
CB A:ASP111 4.9 14.3 1.0
N A:ASP111 4.9 10.9 1.0
N A:ASN110 5.0 10.6 1.0
C A:PHE19 5.0 10.1 1.0
C A:GLY21 5.0 9.5 1.0
N A:THR22 5.0 9.8 1.0

Calcium binding site 2 out of 6 in 3mmz

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Calcium binding site 2 out of 6 in the Crystal Structure of Putative Had Family Hydrolase From Streptomyces Avermitilis Ma-4680


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 Putative Had Family Hydrolase From Streptomyces Avermitilis Ma-4680 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca501

b:10.3
occ:1.00
 O D:ALA138 2.3 10.9 1.0
O D:HOH183 2.3 10.3 1.0
O A:ALA138 2.4 10.9 1.0
O D:GLY136 2.4 9.0 1.0
O A:GLY136 2.4 9.3 1.0
O A:HOH203 2.5 14.2 1.0
O D:HOH215 2.5 13.5 1.0
C D:ALA138 3.5 11.1 1.0
C D:GLY136 3.6 9.8 1.0
C A:ALA138 3.6 10.2 1.0
C A:GLY136 3.6 9.2 1.0
N D:ALA138 4.2 10.4 1.0
C D:ALA137 4.2 11.0 1.0
N A:ALA138 4.2 11.1 1.0
C A:ALA137 4.3 11.5 1.0
O D:ARG135 4.3 11.2 1.0
CA A:GLY136 4.4 9.4 1.0
O A:ARG135 4.4 11.1 1.0
CA D:GLY136 4.4 10.2 1.0
CA D:ALA138 4.4 10.7 1.0
O D:ALA137 4.4 11.1 1.0
CA A:ALA138 4.5 10.7 1.0
N D:ARG139 4.5 11.1 1.0
N D:ALA137 4.5 10.6 1.0
N A:ARG139 4.5 9.1 1.0
O A:ALA137 4.5 11.4 1.0
N A:ALA137 4.6 9.8 1.0
CA D:ARG139 4.6 11.2 1.0
CA A:ARG139 4.6 9.3 1.0
CA D:ALA137 4.7 11.2 1.0
O A:HOH185 4.8 12.8 1.0
CA A:ALA137 4.8 11.2 1.0
O D:HOH188 4.8 17.9 1.0
C D:ARG139 5.0 10.8 1.0

Calcium binding site 3 out of 6 in 3mmz

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Calcium binding site 3 out of 6 in the Crystal Structure of Putative Had Family Hydrolase From Streptomyces Avermitilis Ma-4680


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 Putative Had Family Hydrolase From Streptomyces Avermitilis Ma-4680 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca500

b:13.2
occ:1.00
 O B:HOH309 2.3 19.8 1.0
O B:ASP20 2.3 14.0 1.0
O B:HOH198 2.3 21.7 1.0
OD1 B:ASN110 2.3 12.8 1.0
OD2 B:ASP18 2.4 16.7 1.0
O B:HOH199 2.4 16.8 1.0
CG B:ASP18 3.2 18.1 1.0
OD1 B:ASP18 3.2 15.2 1.0
CG B:ASN110 3.4 14.6 1.0
C B:ASP20 3.5 13.6 1.0
ND2 B:ASN110 3.9 12.8 1.0
OD2 B:ASP114 4.2 14.8 1.0
CA B:ASP20 4.3 12.8 1.0
N B:ASP20 4.4 12.2 1.0
OD1 B:ASP26 4.4 16.2 1.0
CB B:ASP20 4.4 13.7 1.0
O B:HOH545 4.4 37.2 1.0
N B:GLY21 4.5 13.1 1.0
O B:HOH204 4.5 23.9 1.0
CA B:GLY21 4.6 13.0 1.0
OG1 B:THR22 4.6 13.1 1.0
O B:HOH535 4.6 26.8 1.0
CB B:ASP18 4.6 14.3 1.0
NZ B:LYS87 4.6 24.5 1.0
CB B:ASN110 4.7 12.2 1.0
O B:HOH188 4.8 14.3 1.0
CB B:ASP111 4.8 15.2 1.0
N B:THR22 4.9 12.8 1.0
N B:ASP111 4.9 12.2 1.0
C B:PHE19 4.9 12.4 1.0
OD1 B:ASN113 4.9 22.5 1.0
C B:GLY21 4.9 13.0 1.0
N B:ASN110 4.9 11.4 1.0

Calcium binding site 4 out of 6 in 3mmz

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Calcium binding site 4 out of 6 in the Crystal Structure of Putative Had Family Hydrolase From Streptomyces Avermitilis Ma-4680


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 Putative Had Family Hydrolase From Streptomyces Avermitilis Ma-4680 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca501

b:10.5
occ:1.00
 O C:ALA138 2.3 9.7 1.0
O B:ALA138 2.3 12.9 1.0
O C:GLY136 2.4 9.3 1.0
O C:HOH195 2.5 15.6 1.0
O B:GLY136 2.5 11.6 1.0
O B:HOH181 2.5 13.9 1.0
O B:HOH180 2.5 17.8 1.0
C C:GLY136 3.5 9.7 1.0
C C:ALA138 3.6 10.1 1.0
C B:ALA138 3.6 12.9 1.0
C B:GLY136 3.6 11.4 1.0
N C:ALA138 4.1 9.8 1.0
C C:ALA137 4.2 9.4 1.0
N B:ALA138 4.2 12.1 1.0
C B:ALA137 4.3 12.6 1.0
CA C:GLY136 4.3 10.2 1.0
CA B:GLY136 4.4 11.0 1.0
O B:ARG135 4.4 12.5 1.0
CA C:ALA138 4.5 10.3 1.0
O C:ARG135 4.5 10.7 1.0
N B:ARG139 4.5 12.0 1.0
N C:ALA137 4.5 9.1 1.0
O C:ALA137 4.5 9.6 1.0
CA B:ALA138 4.5 12.4 1.0
N C:ARG139 4.5 10.5 1.0
CA B:ARG139 4.5 12.5 1.0
O B:ALA137 4.5 12.5 1.0
N B:ALA137 4.5 11.7 1.0
O B:HOH195 4.6 14.6 1.0
CA C:ARG139 4.6 11.3 1.0
CA C:ALA137 4.6 8.8 1.0
CA B:ALA137 4.7 12.1 1.0
C B:ARG139 4.9 12.4 1.0

Calcium binding site 5 out of 6 in 3mmz

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Calcium binding site 5 out of 6 in the Crystal Structure of Putative Had Family Hydrolase From Streptomyces Avermitilis Ma-4680


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 Putative Had Family Hydrolase From Streptomyces Avermitilis Ma-4680 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca500

b:10.8
occ:1.00
 OD2 C:ASP18 2.3 14.5 1.0
O C:ASP20 2.3 10.9 1.0
OD1 C:ASN110 2.3 11.5 1.0
O C:HOH207 2.4 22.8 1.0
O C:HOH178 2.4 14.2 1.0
O C:HOH191 2.5 15.2 1.0
CG C:ASP18 3.1 17.2 1.0
OD1 C:ASP18 3.3 14.6 1.0
CG C:ASN110 3.4 9.8 1.0
C C:ASP20 3.5 11.3 1.0
ND2 C:ASN110 3.9 10.6 1.0
O C:HOH210 4.2 25.3 1.0
CA C:ASP20 4.3 12.3 1.0
OD2 C:ASP114 4.4 13.0 1.0
N C:ASP20 4.4 11.4 1.0
N C:GLY21 4.5 10.9 1.0
CB C:ASP20 4.5 15.1 1.0
CB C:ASP18 4.5 13.1 1.0
OG1 C:THR22 4.6 11.6 1.0
CA C:GLY21 4.6 10.2 1.0
CB C:ASP111 4.7 15.1 1.0
CB C:ASN110 4.7 9.9 1.0
OD1 C:ASP26 4.8 16.9 1.0
ND2 C:ASN113 4.8 16.5 1.0
O C:HOH204 4.9 27.3 1.0
C C:PHE19 4.9 11.8 1.0
N C:ASN110 5.0 9.7 1.0
N C:THR22 5.0 9.9 1.0
C C:GLY21 5.0 10.3 1.0

Calcium binding site 6 out of 6 in 3mmz

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Calcium binding site 6 out of 6 in the Crystal Structure of Putative Had Family Hydrolase From Streptomyces Avermitilis Ma-4680


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 Putative Had Family Hydrolase From Streptomyces Avermitilis Ma-4680 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca500

b:14.0
occ:1.00
 O D:ASP20 2.3 13.3 1.0
OD1 D:ASN110 2.3 13.4 1.0
O D:HOH437 2.3 22.6 1.0
O D:HOH191 2.3 15.0 1.0
O B:HOH217 2.4 17.0 1.0
OD2 D:ASP18 2.4 16.0 1.0
CG D:ASP18 3.2 10.7 1.0
OD1 D:ASP18 3.3 15.7 1.0
CG D:ASN110 3.4 17.8 1.0
C D:ASP20 3.5 13.8 1.0
ND2 D:ASN110 3.9 13.1 1.0
OD2 D:ASP114 4.2 13.7 1.0
CA D:ASP20 4.3 14.7 1.0
N D:ASP20 4.5 14.1 1.0
N D:GLY21 4.5 13.2 1.0
CB D:ASP20 4.5 16.3 1.0
CA D:GLY21 4.6 13.1 1.0
OG1 D:THR22 4.6 13.7 1.0
O D:HOH441 4.6 29.7 1.0
CB D:ASP18 4.6 15.4 1.0
O D:HOH340 4.7 25.3 1.0
CB D:ASN110 4.7 12.7 1.0
CB D:ASP111 4.7 18.1 1.0
OD1 D:ASP26 4.7 16.2 1.0
OD1 D:ASN113 4.8 19.8 1.0
NH2 B:ARG42 4.9 34.3 1.0
N D:ASP111 4.9 13.7 1.0
N D:ASN110 5.0 12.2 1.0
C D:PHE19 5.0 13.9 1.0
C D:GLY21 5.0 12.5 1.0

Reference:

K.D.Daughtry, H.Huang, V.Malashkevich, Y.Patskovsky, W.Liu, U.Ramagopal, J.M.Sauder, S.K.Burley, S.C.Almo, D.Dunaway-Mariano, K.N.Allen. Structural Basis For the Divergence of Substrate Specificity and Biological Function Within Had Phosphatases in Lipopolysaccharide and Sialic Acid Biosynthesis. Biochemistry V. 52 5372 2013.
ISSN: ISSN 0006-2960
PubMed: 23848398
DOI: 10.1021/BI400659K
Page generated: Sat Jul 13 13:41:35 2024

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