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Cobalt in PDB 2dds: Crystal Structure of Sphingomyelinase From Bacillus Cereus with Cobalt Ion

Enzymatic activity of Crystal Structure of Sphingomyelinase From Bacillus Cereus with Cobalt Ion

All present enzymatic activity of Crystal Structure of Sphingomyelinase From Bacillus Cereus with Cobalt Ion:
3.1.4.12;

Protein crystallography data

The structure of Crystal Structure of Sphingomyelinase From Bacillus Cereus with Cobalt Ion, PDB code: 2dds was solved by H.Ago, M.Oda, M.Takahashi, H.Tsuge, S.Ochi, N.Katunuma, M.Miyano, J.Sakurai, Riken Structural Genomics/Proteomics Initiative(Rsgi), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.67 / 1.80
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 65.090, 72.670, 78.060, 112.00, 90.05, 116.58
R / Rfree (%) 20.2 / 23.2

Cobalt Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Cobalt atom in the Crystal Structure of Sphingomyelinase From Bacillus Cereus with Cobalt Ion (pdb code 2dds). This binding sites where shown within 5.0 Angstroms radius around Cobalt atom.
In total 12 binding sites of Cobalt where determined in the Crystal Structure of Sphingomyelinase From Bacillus Cereus with Cobalt Ion, PDB code: 2dds:
Jump to Cobalt binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Cobalt binding site 1 out of 12 in 2dds

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Cobalt binding site 1 out of 12 in the Crystal Structure of Sphingomyelinase From Bacillus Cereus with Cobalt Ion


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 1 of Crystal Structure of Sphingomyelinase From Bacillus Cereus with Cobalt Ion within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Co1117

b:21.6
occ:1.00
 O A:HOH1130 2.0 9.2 1.0
OE1 A:GLU53 2.1 8.8 1.0
O A:HOH1144 2.2 12.8 1.0
O A:HOH1141 2.2 12.5 1.0
O A:HOH1138 2.3 12.8 1.0
O A:HOH1229 2.5 18.9 1.0
CD A:GLU53 2.9 10.2 1.0
OE2 A:GLU53 3.1 13.5 1.0
CO A:CO1127 3.5 63.3 1.0
ND2 A:ASN16 4.1 8.2 1.0
O A:HOH1183 4.2 20.6 1.0
OD2 A:ASP295 4.2 13.9 1.0
CD1 A:TYR18 4.2 11.8 1.0
O A:HOH1407 4.3 9.1 1.0
NE2 A:HIS296 4.3 8.0 1.0
OD1 A:ASN16 4.3 8.8 1.0
CG A:GLU53 4.3 8.4 1.0
O A:HOH1406 4.5 26.9 1.0
OD1 A:ASP295 4.5 10.6 1.0
CD2 A:HIS296 4.5 8.9 1.0
CG A:ASN16 4.6 8.2 1.0
CE1 A:TYR18 4.6 13.0 1.0
CG A:ASP295 4.8 10.9 1.0
O A:HOH1392 4.8 64.5 1.0
O A:HOH1135 5.0 11.4 1.0

Cobalt binding site 2 out of 12 in 2dds

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Cobalt binding site 2 out of 12 in the Crystal Structure of Sphingomyelinase From Bacillus Cereus with Cobalt Ion


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 2 of Crystal Structure of Sphingomyelinase From Bacillus Cereus with Cobalt Ion within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Co1121

b:19.5
occ:1.00
 OE1 A:GLU99 2.0 13.9 1.0
OD2 A:ASP100 2.2 15.4 1.0
O A:PHE55 2.2 11.1 1.0
O A:HOH1168 2.2 13.8 1.0
OD1 A:ASN57 2.2 15.8 1.0
O A:HOH1159 2.3 15.6 1.0
CD A:GLU99 3.1 16.8 1.0
CG A:ASP100 3.1 13.0 1.0
C A:PHE55 3.3 11.4 1.0
CG A:ASN57 3.4 15.7 1.0
OE2 A:GLU99 3.5 17.0 1.0
OD1 A:ASP100 3.7 11.2 1.0
NH2 A:ARG80 3.9 9.8 1.0
N A:ASN57 4.0 12.3 1.0
ND2 A:ASN57 4.0 18.1 1.0
N A:ASP100 4.0 11.3 1.0
CA A:PHE55 4.0 10.3 1.0
O A:HOH1415 4.1 27.4 1.0
NE A:ARG80 4.1 12.5 1.0
CB A:ASP100 4.2 11.6 1.0
N A:ASP56 4.3 10.3 1.0
CZ A:ARG80 4.3 14.8 1.0
CG A:GLU99 4.4 12.8 1.0
C A:ASP56 4.4 11.2 1.0
CB A:ASN57 4.5 14.4 1.0
CA A:ASN57 4.5 11.9 1.0
CA A:ASP56 4.5 10.5 1.0
CB A:PHE55 4.6 11.0 1.0
CA A:ASP100 4.7 11.0 1.0
O A:HOH1266 4.9 23.3 1.0
CA A:GLU99 4.9 12.5 1.0
O A:HOH1416 4.9 61.4 1.0
C A:GLU99 5.0 12.2 1.0

Cobalt binding site 3 out of 12 in 2dds

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Cobalt binding site 3 out of 12 in the Crystal Structure of Sphingomyelinase From Bacillus Cereus with Cobalt Ion


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 3 of Crystal Structure of Sphingomyelinase From Bacillus Cereus with Cobalt Ion within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Co1127

b:63.3
occ:1.00
 O A:HOH1130 2.0 9.2 1.0
O A:HOH1164 2.0 12.9 1.0
NE2 A:HIS296 2.2 8.0 1.0
O A:HOH1135 2.5 11.4 1.0
CE1 A:HIS296 3.1 7.3 1.0
CD2 A:HIS296 3.3 8.9 1.0
O A:HOH1141 3.3 12.5 1.0
O A:HOH1392 3.4 64.5 1.0
O A:HOH1406 3.5 26.9 1.0
CO A:CO1117 3.5 21.6 1.0
CD1 A:TRP232 3.9 15.3 1.0
OD1 A:ASP195 4.1 10.5 1.0
NE1 A:TRP232 4.1 16.9 1.0
OD2 A:ASP295 4.2 13.9 1.0
ND1 A:HIS296 4.2 10.1 1.0
O A:HOH1138 4.3 12.8 1.0
O A:HOH1229 4.3 18.9 1.0
O A:HOH1407 4.4 9.1 1.0
CG A:HIS296 4.4 8.7 1.0
CG A:TRP232 4.4 16.3 1.0
CE2 A:TRP232 4.6 17.7 1.0
O A:HOH1209 4.7 21.6 1.0
CD1 A:LEU252 4.7 11.3 1.0
ND2 A:ASN16 4.7 8.2 1.0
CD2 A:TRP232 4.8 16.4 1.0
OD1 A:ASN197 4.8 14.9 1.0
OE1 A:GLU53 4.8 8.8 1.0

Cobalt binding site 4 out of 12 in 2dds

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Cobalt binding site 4 out of 12 in the Crystal Structure of Sphingomyelinase From Bacillus Cereus with Cobalt Ion


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 4 of Crystal Structure of Sphingomyelinase From Bacillus Cereus with Cobalt Ion within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Co1118

b:19.4
occ:1.00
 O B:HOH1349 2.0 14.7 1.0
OE1 B:GLU53 2.1 9.0 1.0
O B:HOH1136 2.1 10.2 1.0
O B:HOH1135 2.3 11.8 1.0
O B:HOH1140 2.3 14.2 1.0
O B:HOH1167 2.4 17.8 1.0
CD B:GLU53 3.0 12.2 1.0
OE2 B:GLU53 3.1 13.9 1.0
CO B:CO1125 3.4 0.1 1.0
ND2 B:ASN16 4.0 9.4 1.0
O B:HOH1157 4.1 26.9 1.0
OD2 B:ASP295 4.2 15.4 1.0
O B:HOH1350 4.3 20.1 1.0
CD1 B:TYR18 4.3 13.9 1.0
OD1 B:ASN16 4.4 9.2 1.0
O B:HOH1363 4.4 7.2 1.0
CG B:GLU53 4.4 9.7 1.0
NE2 B:HIS296 4.4 12.3 1.0
CD2 B:HIS296 4.4 12.4 1.0
O B:HOH1338 4.4 25.2 1.0
OD1 B:ASP295 4.5 12.5 1.0
CG B:ASN16 4.6 9.6 1.0
CE1 B:TYR18 4.7 14.7 1.0
CG B:ASP295 4.8 14.2 1.0
O B:HOH1139 4.9 14.9 1.0

Cobalt binding site 5 out of 12 in 2dds

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Cobalt binding site 5 out of 12 in the Crystal Structure of Sphingomyelinase From Bacillus Cereus with Cobalt Ion


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 5 of Crystal Structure of Sphingomyelinase From Bacillus Cereus with Cobalt Ion within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Co1122

b:20.3
occ:1.00
 OE1 B:GLU99 2.0 18.2 1.0
OD2 B:ASP100 2.1 17.2 1.0
O B:PHE55 2.2 10.1 1.0
O B:HOH1148 2.2 14.5 1.0
O B:HOH1203 2.3 21.8 1.0
OD1 B:ASN57 2.3 15.5 1.0
CD B:GLU99 3.1 17.8 1.0
CG B:ASP100 3.1 13.7 1.0
C B:PHE55 3.3 9.1 1.0
CG B:ASN57 3.3 14.4 1.0
OE2 B:GLU99 3.5 18.5 1.0
OD1 B:ASP100 3.8 12.7 1.0
ND2 B:ASN57 3.9 13.7 1.0
NH2 B:ARG80 3.9 11.3 1.0
CA B:PHE55 4.0 10.9 1.0
N B:ASN57 4.0 11.4 1.0
N B:ASP100 4.1 10.9 1.0
NE B:ARG80 4.1 16.2 1.0
CB B:ASP100 4.1 11.7 1.0
O B:HOH1170 4.2 19.5 1.0
O B:HOH1359 4.2 33.5 1.0
N B:ASP56 4.3 11.0 1.0
CZ B:ARG80 4.4 15.7 1.0
CG B:GLU99 4.4 13.9 1.0
C B:ASP56 4.5 10.6 1.0
CB B:ASN57 4.5 14.0 1.0
CB B:PHE55 4.5 9.3 1.0
CA B:ASP56 4.6 10.2 1.0
CA B:ASN57 4.6 11.3 1.0
CA B:ASP100 4.7 11.9 1.0
O B:HOH1318 4.8 32.4 1.0
CA B:GLU99 4.9 11.7 1.0

Cobalt binding site 6 out of 12 in 2dds

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Cobalt binding site 6 out of 12 in the Crystal Structure of Sphingomyelinase From Bacillus Cereus with Cobalt Ion


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 6 of Crystal Structure of Sphingomyelinase From Bacillus Cereus with Cobalt Ion within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Co1125

b:0.1
occ:1.00
 O B:HOH1349 2.0 14.7 1.0
O B:HOH1133 2.1 15.8 1.0
O B:HOH1350 2.5 20.1 1.0
NE2 B:HIS296 2.5 12.3 1.0
O B:HOH1139 2.5 14.9 1.0
O B:HOH1140 3.0 14.2 1.0
CO B:CO1118 3.4 19.4 1.0
CD2 B:HIS296 3.4 12.4 1.0
CE1 B:HIS296 3.5 12.3 1.0
O B:HOH1167 4.0 17.8 1.0
NE1 B:TRP232 4.0 14.0 1.0
CD1 B:TRP232 4.0 14.3 1.0
OD2 B:ASP295 4.2 15.4 1.0
O B:HOH1333 4.2 45.5 1.0
O B:HOH1363 4.2 7.2 1.0
O B:HOH1135 4.2 11.8 1.0
OD1 B:ASP195 4.2 12.3 1.0
CE2 B:TRP232 4.5 15.6 1.0
CG B:TRP232 4.5 15.3 1.0
ND1 B:HIS296 4.6 13.3 1.0
CG B:HIS296 4.6 11.8 1.0
O B:HOH1313 4.6 25.0 1.0
CD2 B:TRP232 4.7 14.8 1.0
OE1 B:GLU53 4.7 9.0 1.0
ND2 B:ASN16 4.8 9.4 1.0
OD1 B:ASN197 4.9 13.7 1.0
CD1 B:LEU252 4.9 10.3 1.0

Cobalt binding site 7 out of 12 in 2dds

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Cobalt binding site 7 out of 12 in the Crystal Structure of Sphingomyelinase From Bacillus Cereus with Cobalt Ion


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 7 of Crystal Structure of Sphingomyelinase From Bacillus Cereus with Cobalt Ion within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Co1119

b:21.5
occ:1.00
 O C:HOH1136 2.1 11.8 1.0
OE1 C:GLU53 2.1 11.4 1.0
O C:HOH1132 2.2 10.7 1.0
O C:HOH1141 2.2 13.6 1.0
O C:HOH1155 2.3 16.2 1.0
O C:HOH1240 2.4 23.7 1.0
CD C:GLU53 2.9 12.7 1.0
OE2 C:GLU53 3.1 14.1 1.0
CO C:CO1126 3.7 64.0 1.0
O C:HOH1181 4.1 19.8 1.0
CD1 C:TYR18 4.1 11.6 1.0
OD2 C:ASP295 4.2 14.4 1.0
ND2 C:ASN16 4.2 9.6 1.0
O C:HOH1383 4.3 7.0 1.0
CG C:GLU53 4.3 11.4 1.0
OD1 C:ASN16 4.4 23.8 1.0
OD1 C:ASP295 4.5 10.7 1.0
NE2 C:HIS296 4.5 10.9 1.0
CE1 C:TYR18 4.6 13.6 1.0
O C:HOH1352 4.6 26.0 1.0
CD2 C:HIS296 4.6 10.8 1.0
O C:HOH1379 4.6 30.1 1.0
CG C:ASN16 4.6 14.1 1.0
O C:HOH1351 4.8 30.9 1.0
CG C:ASP295 4.8 11.6 1.0
O C:HOH1358 4.9 68.0 1.0
O C:HOH1137 5.0 11.1 1.0

Cobalt binding site 8 out of 12 in 2dds

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Cobalt binding site 8 out of 12 in the Crystal Structure of Sphingomyelinase From Bacillus Cereus with Cobalt Ion


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 8 of Crystal Structure of Sphingomyelinase From Bacillus Cereus with Cobalt Ion within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Co1123

b:19.5
occ:1.00
 OE1 C:GLU99 2.1 14.2 1.0
O C:PHE55 2.1 11.3 1.0
O C:HOH1175 2.1 16.2 1.0
OD2 C:ASP100 2.2 15.8 1.0
OD1 C:ASN57 2.2 15.8 1.0
O C:HOH1172 2.2 18.2 1.0
CD C:GLU99 3.1 15.6 1.0
CG C:ASP100 3.1 12.8 1.0
C C:PHE55 3.2 11.2 1.0
CG C:ASN57 3.3 16.8 1.0
OE2 C:GLU99 3.5 15.3 1.0
OD1 C:ASP100 3.7 11.7 1.0
NH2 C:ARG80 3.9 10.9 1.0
N C:ASN57 3.9 11.8 1.0
ND2 C:ASN57 3.9 17.2 1.0
CA C:PHE55 4.0 10.2 1.0
NE C:ARG80 4.1 12.1 1.0
N C:ASP100 4.1 11.1 1.0
CB C:ASP100 4.2 11.5 1.0
O C:HOH1270 4.2 29.6 1.0
N C:ASP56 4.3 10.7 1.0
CZ C:ARG80 4.3 14.3 1.0
C C:ASP56 4.4 10.9 1.0
CG C:GLU99 4.4 12.3 1.0
CB C:ASN57 4.5 13.7 1.0
CA C:ASP56 4.5 9.6 1.0
CA C:ASN57 4.5 12.3 1.0
O C:HOH1290 4.5 33.7 1.0
CB C:PHE55 4.6 10.8 1.0
CA C:ASP100 4.8 10.7 1.0
CA C:GLU99 5.0 11.8 1.0

Cobalt binding site 9 out of 12 in 2dds

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Cobalt binding site 9 out of 12 in the Crystal Structure of Sphingomyelinase From Bacillus Cereus with Cobalt Ion


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 9 of Crystal Structure of Sphingomyelinase From Bacillus Cereus with Cobalt Ion within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Co1126

b:64.0
occ:1.00
 O C:HOH1152 2.0 12.6 1.0
O C:HOH1136 2.1 11.8 1.0
NE2 C:HIS296 2.2 10.9 1.0
O C:HOH1137 2.3 11.1 1.0
CE1 C:HIS296 3.1 8.6 1.0
CD2 C:HIS296 3.3 10.8 1.0
O C:HOH1358 3.4 68.0 1.0
O C:HOH1155 3.5 16.2 1.0
O C:HOH1379 3.5 30.1 1.0
CO C:CO1119 3.7 21.5 1.0
OD1 C:ASP195 4.0 9.2 1.0
CD1 C:TRP232 4.0 15.5 1.0
NE1 C:TRP232 4.2 16.6 1.0
O C:HOH1383 4.2 7.0 1.0
ND1 C:HIS296 4.3 10.3 1.0
O C:HOH1240 4.3 23.7 1.0
CG C:HIS296 4.4 9.2 1.0
CG C:TRP232 4.4 17.0 1.0
O C:HOH1141 4.4 13.6 1.0
OD2 C:ASP295 4.5 14.4 1.0
CD1 C:LEU252 4.6 11.8 1.0
O C:HOH1210 4.6 20.0 1.0
OD1 C:ASN197 4.7 13.9 1.0
CE2 C:TRP232 4.7 18.1 1.0
CD2 C:TRP232 4.8 16.7 1.0
OE1 C:GLU53 4.9 11.4 1.0
CG C:ASP195 5.0 11.7 1.0
OD1 C:ASN16 5.0 23.8 1.0

Cobalt binding site 10 out of 12 in 2dds

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Cobalt binding site 10 out of 12 in the Crystal Structure of Sphingomyelinase From Bacillus Cereus with Cobalt Ion


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 10 of Crystal Structure of Sphingomyelinase From Bacillus Cereus with Cobalt Ion within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Co1120

b:20.1
occ:1.00
 O D:HOH1143 2.1 13.5 1.0
OE1 D:GLU53 2.1 12.7 1.0
O D:HOH1133 2.1 9.7 1.0
O D:HOH1134 2.2 10.3 1.0
O D:HOH1152 2.3 14.2 1.0
O D:HOH1183 2.3 16.5 1.0
CD D:GLU53 2.9 14.1 1.0
OE2 D:GLU53 3.1 15.6 1.0
CO D:CO1128 3.5 88.4 1.0
O D:HOH1222 4.0 29.5 1.0
ND2 D:ASN16 4.0 9.2 1.0
OD2 D:ASP295 4.2 15.7 1.0
OD1 D:ASN16 4.3 9.6 1.0
CD1 D:TYR18 4.3 14.1 1.0
CG D:GLU53 4.3 11.7 1.0
O D:HOH1369 4.4 7.1 1.0
O D:HOH1353 4.4 21.1 1.0
NE2 D:HIS296 4.4 12.2 1.0
OD1 D:ASP295 4.4 14.2 1.0
CD2 D:HIS296 4.5 11.9 1.0
O D:HOH1352 4.5 21.8 1.0
CG D:ASN16 4.5 8.0 1.0
CE1 D:TYR18 4.7 14.7 1.0
CG D:ASP295 4.7 14.3 1.0
O D:HOH1316 4.8 27.1 1.0

Reference:

H.Ago, M.Oda, M.Takahashi, H.Tsuge, S.Ochi, N.Katunuma, M.Miyano, J.Sakurai. Structural Basis of the Sphingomyelin Phosphodiesterase Activity in Neutral Sphingomyelinase From Bacillus Cereus. J.Biol.Chem. V. 281 16157 2006.
ISSN: ISSN 0021-9258
PubMed: 16595670
DOI: 10.1074/JBC.M601089200
Page generated: Tue Jul 30 15:00:58 2024

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