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Cobalt in PDB 5zt7: Sirb From Bacillus Subtilis with CO2+

Enzymatic activity of Sirb From Bacillus Subtilis with CO2+

All present enzymatic activity of Sirb From Bacillus Subtilis with CO2+:
4.99.1.4;

Protein crystallography data

The structure of Sirb From Bacillus Subtilis with CO2+, PDB code: 5zt7 was solved by T.Fujishiro, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 36.85 / 2.94
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 64.960, 52.090, 75.470, 90.00, 112.09, 90.00
R / Rfree (%) 24.6 / 27.6

Cobalt Binding Sites:

The binding sites of Cobalt atom in the Sirb From Bacillus Subtilis with CO2+ (pdb code 5zt7). This binding sites where shown within 5.0 Angstroms radius around Cobalt atom.
In total 9 binding sites of Cobalt where determined in the Sirb From Bacillus Subtilis with CO2+, PDB code: 5zt7:
Jump to Cobalt binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Cobalt binding site 1 out of 9 in 5zt7

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Cobalt binding site 1 out of 9 in the Sirb From Bacillus Subtilis with CO2+


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 1 of Sirb From Bacillus Subtilis with CO2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Co301

b:0.8
occ:1.00
 NZ A:LYS231 1.9 0.5 1.0
NE2 A:HIS31 2.4 81.5 1.0
CE A:LYS231 3.3 0.2 1.0
CE1 A:HIS31 3.3 85.8 1.0
CD2 A:HIS31 3.4 74.3 1.0
O A:GLY27 3.9 74.4 1.0
CD A:LYS231 4.3 98.8 1.0
ND1 A:HIS31 4.5 77.9 1.0
CG A:HIS31 4.5 75.6 1.0
C A:GLY27 4.7 72.0 1.0

Cobalt binding site 2 out of 9 in 5zt7

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Cobalt binding site 2 out of 9 in the Sirb From Bacillus Subtilis with CO2+


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 2 of Sirb From Bacillus Subtilis with CO2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Co302

b:0.3
occ:1.00
 NE2 A:HIS79 1.8 0.7 1.0
OE1 A:GLU83 1.9 0.3 1.0
CE1 A:HIS79 2.5 0.1 1.0
O A:HOH407 2.5 0.0 1.0
CD A:GLU83 2.9 0.1 1.0
CD2 A:HIS79 3.0 0.4 1.0
O A:HOH401 3.1 0.8 1.0
OE2 A:GLU83 3.2 0.1 1.0
ND1 A:HIS79 3.7 0.6 1.0
CG A:HIS79 4.0 0.2 1.0
CG A:GLU83 4.2 0.7 1.0
CB A:GLU83 4.5 0.8 1.0

Cobalt binding site 3 out of 9 in 5zt7

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Cobalt binding site 3 out of 9 in the Sirb From Bacillus Subtilis with CO2+


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 3 of Sirb From Bacillus Subtilis with CO2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Co303

b:0.1
occ:1.00
 NE2 A:HIS229 2.3 0.7 1.0
O A:HOH406 2.3 0.9 1.0
NE2 A:HIS115 2.3 0.2 1.0
O A:HOH405 2.5 0.1 1.0
CE1 A:HIS115 2.7 0.2 1.0
CE1 A:HIS229 2.9 0.1 1.0
CD2 A:HIS229 3.4 0.8 1.0
CD2 A:HIS115 3.6 0.3 1.0
ND1 A:HIS115 3.9 0.8 1.0
ND1 A:HIS229 4.2 95.4 1.0
CG A:HIS115 4.4 0.3 1.0
CG A:HIS229 4.4 98.2 1.0
CB A:LYS111 4.9 0.4 1.0
CD A:LYS111 4.9 98.5 1.0

Cobalt binding site 4 out of 9 in 5zt7

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Cobalt binding site 4 out of 9 in the Sirb From Bacillus Subtilis with CO2+


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 4 of Sirb From Bacillus Subtilis with CO2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Co304

b:73.1
occ:1.00
 NE2 A:HIS10 2.0 78.9 1.0
NE2 A:HIS76 2.0 75.9 1.0
O A:HOH404 2.6 81.1 1.0
CE1 A:HIS76 2.8 77.2 1.0
CE1 A:HIS10 2.9 74.2 1.0
CD2 A:HIS10 3.0 70.8 1.0
OE2 A:GLU43 3.1 68.3 1.0
CD2 A:HIS76 3.1 76.3 1.0
ND1 A:HIS76 4.0 80.6 1.0
ND1 A:HIS10 4.0 69.9 1.0
CD A:GLU43 4.1 69.9 1.0
CG A:HIS10 4.1 69.6 1.0
CG A:HIS76 4.1 78.2 1.0
OE1 A:GLU43 4.6 68.9 1.0

Cobalt binding site 5 out of 9 in 5zt7

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Cobalt binding site 5 out of 9 in the Sirb From Bacillus Subtilis with CO2+


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 5 of Sirb From Bacillus Subtilis with CO2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Co301

b:0.1
occ:1.00
 NE2 B:HIS31 1.9 1.0 1.0
CE1 B:HIS31 2.0 0.8 1.0
O B:HOH422 3.1 0.0 1.0
CD2 B:HIS31 3.2 0.8 1.0
ND1 B:HIS31 3.4 0.5 1.0
NZ B:LYS231 3.5 1.0 1.0
CG B:HIS31 3.9 0.1 1.0
CE B:LYS231 4.0 92.7 1.0
O B:GLY27 4.6 90.9 1.0
CD B:LYS231 4.9 85.8 1.0

Cobalt binding site 6 out of 9 in 5zt7

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Cobalt binding site 6 out of 9 in the Sirb From Bacillus Subtilis with CO2+


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 6 of Sirb From Bacillus Subtilis with CO2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Co302

b:0.8
occ:1.00
 O B:HOH417 2.3 92.2 1.0
O B:HOH423 2.3 0.6 1.0
NE2 B:HIS214 2.4 88.4 1.0
O B:HOH409 2.5 94.8 1.0
CE1 B:HIS214 3.0 88.5 1.0
CD2 B:HIS214 3.7 83.1 1.0
ND1 B:HIS214 4.2 85.9 1.0
CG B:HIS214 4.6 83.7 1.0
OE2 B:GLU181 4.9 85.8 1.0

Cobalt binding site 7 out of 9 in 5zt7

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Cobalt binding site 7 out of 9 in the Sirb From Bacillus Subtilis with CO2+


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 7 of Sirb From Bacillus Subtilis with CO2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Co303

b:0.3
occ:1.00
 NE2 B:HIS79 2.0 0.7 1.0
OE2 B:GLU83 2.2 0.9 1.0
CE1 B:HIS79 2.6 0.2 1.0
O B:HOH418 3.0 0.5 1.0
CD B:GLU83 3.0 0.7 1.0
O B:HOH406 3.1 0.1 1.0
OE1 B:GLU83 3.2 0.2 1.0
CD2 B:HIS79 3.3 0.9 1.0
ND1 B:HIS79 3.9 0.1 1.0
CG B:HIS79 4.2 0.2 1.0
CG B:GLU83 4.4 0.9 1.0

Cobalt binding site 8 out of 9 in 5zt7

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Cobalt binding site 8 out of 9 in the Sirb From Bacillus Subtilis with CO2+


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 8 of Sirb From Bacillus Subtilis with CO2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Co304

b:82.8
occ:1.00
 O B:HOH412 2.1 79.8 1.0
NE2 B:HIS229 2.2 84.8 1.0
NE2 B:HIS115 2.3 82.0 1.0
O B:HOH421 2.3 92.6 1.0
CE1 B:HIS115 2.7 82.5 1.0
CE1 B:HIS229 2.8 84.6 1.0
CD2 B:HIS229 3.4 80.6 1.0
CD2 B:HIS115 3.5 81.0 1.0
ND1 B:HIS115 3.9 83.7 1.0
ND1 B:HIS229 4.1 79.9 1.0
CG B:HIS115 4.3 80.2 1.0
CG B:HIS229 4.4 77.3 1.0

Cobalt binding site 9 out of 9 in 5zt7

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Cobalt binding site 9 out of 9 in the Sirb From Bacillus Subtilis with CO2+


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 9 of Sirb From Bacillus Subtilis with CO2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Co305

b:68.5
occ:1.00
 NE2 B:HIS10 1.9 70.8 1.0
O B:HOH401 2.2 64.3 1.0
NE2 B:HIS76 2.4 66.8 1.0
OE1 B:GLU43 2.4 99.0 1.0
CE1 B:HIS10 2.6 70.3 1.0
CD2 B:HIS10 3.1 66.3 1.0
CE1 B:HIS76 3.2 67.6 1.0
CD2 B:HIS76 3.4 64.9 1.0
CD B:GLU43 3.5 90.9 1.0
ND1 B:HIS10 3.7 70.7 1.0
CG B:HIS10 4.0 70.8 1.0
OE2 B:GLU43 4.1 97.9 1.0
ND1 B:HIS76 4.4 68.6 1.0
CG B:HIS76 4.5 66.6 1.0
CG B:GLU43 4.7 82.1 1.0

Reference:

T.Fujishiro, Y.Shimada, R.Nakamura, M.Ooi. Structure of Sirohydrochlorin Ferrochelatase Sirb: the Last of the Structures of the Class II Chelatase Family. Dalton Trans V. 48 6083 2019.
ISSN: ESSN 1477-9234
PubMed: 30778451
DOI: 10.1039/C8DT04727H
Page generated: Tue Jul 30 18:26:56 2024

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