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Cobalt in PDB 3oce: Crystal Structure of Fumarate Lyase:Delta Crystallin From Brucella Melitensis Bound to Cobalt

Enzymatic activity of Crystal Structure of Fumarate Lyase:Delta Crystallin From Brucella Melitensis Bound to Cobalt

All present enzymatic activity of Crystal Structure of Fumarate Lyase:Delta Crystallin From Brucella Melitensis Bound to Cobalt:
4.3.1.1;

Protein crystallography data

The structure of Crystal Structure of Fumarate Lyase:Delta Crystallin From Brucella Melitensis Bound to Cobalt, PDB code: 3oce was solved by Seattle Structural Genomics Center For Infectious Disease (Ssgcid), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 2.58
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 95.330, 113.550, 236.860, 90.00, 90.00, 90.00
R / Rfree (%) 19.6 / 24.5

Other elements in 3oce:

The structure of Crystal Structure of Fumarate Lyase:Delta Crystallin From Brucella Melitensis Bound to Cobalt also contains other interesting chemical elements:

Chlorine (Cl) 4 atoms

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 Fumarate Lyase:Delta Crystallin From Brucella Melitensis Bound to Cobalt (pdb code 3oce). 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 Fumarate Lyase:Delta Crystallin From Brucella Melitensis Bound to Cobalt, PDB code: 3oce:
Jump to Cobalt binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Cobalt binding site 1 out of 12 in 3oce

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Cobalt binding site 1 out of 12 in the Crystal Structure of Fumarate Lyase:Delta Crystallin From Brucella Melitensis Bound to Cobalt


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 Fumarate Lyase:Delta Crystallin From Brucella Melitensis Bound to Cobalt within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Co471

b:9.9
occ:1.00
 OD2 A:ASP269 1.9 17.3 1.0
OE2 A:GLU265 2.1 22.1 1.0
OE2 D:GLU209 2.1 15.7 1.0
O A:HOH476 2.2 5.0 1.0
OE1 D:GLU209 2.2 17.4 1.0
CD D:GLU209 2.5 19.4 1.0
CD A:GLU265 3.0 20.5 1.0
CG A:ASP269 3.0 19.8 1.0
OE1 A:GLU265 3.2 21.6 1.0
CB A:ASP269 3.6 19.2 1.0
O A:HOH477 4.0 14.2 1.0
O A:HOH478 4.0 11.2 1.0
CG D:GLU209 4.0 20.9 1.0
OG1 D:THR206 4.0 16.9 1.0
OD1 A:ASP269 4.1 18.4 1.0
O D:HOH585 4.1 36.0 1.0
CG A:GLU265 4.4 20.0 1.0
NZ D:LYS286 4.7 19.5 1.0
O A:HOH566 4.7 12.3 1.0
O D:HOH515 4.8 5.9 1.0
O A:ASP269 4.9 19.7 1.0
CB D:GLU209 4.9 21.9 1.0

Cobalt binding site 2 out of 12 in 3oce

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Cobalt binding site 2 out of 12 in the Crystal Structure of Fumarate Lyase:Delta Crystallin From Brucella Melitensis Bound to Cobalt


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 Fumarate Lyase:Delta Crystallin From Brucella Melitensis Bound to Cobalt within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Co472

b:38.7
occ:1.00
 O A:HOH496 1.9 27.2 1.0
NE2 A:HIS40 2.1 33.5 1.0
O A:HOH497 2.3 35.5 1.0
CE1 A:HIS40 3.0 33.9 1.0
CD2 A:HIS40 3.2 31.4 1.0
OD1 A:ASN39 4.0 25.1 1.0
O A:ASP35 4.0 28.2 1.0
ND1 A:HIS40 4.2 32.2 1.0
CG A:HIS40 4.3 28.6 1.0
N A:ALA37 5.0 23.1 1.0

Cobalt binding site 3 out of 12 in 3oce

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Cobalt binding site 3 out of 12 in the Crystal Structure of Fumarate Lyase:Delta Crystallin From Brucella Melitensis Bound to Cobalt


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 Fumarate Lyase:Delta Crystallin From Brucella Melitensis Bound to Cobalt within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Co473

b:56.7
occ:1.00
 NE2 A:HIS164 2.5 30.0 1.0
CE1 A:HIS164 3.3 27.8 1.0
CD2 A:HIS164 3.5 28.1 1.0
O A:HOH608 3.7 25.7 1.0
ND1 A:HIS164 4.5 27.4 1.0
CG A:HIS164 4.6 25.4 1.0
OG1 A:THR211 4.9 21.2 1.0

Cobalt binding site 4 out of 12 in 3oce

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Cobalt binding site 4 out of 12 in the Crystal Structure of Fumarate Lyase:Delta Crystallin From Brucella Melitensis Bound to Cobalt


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 Fumarate Lyase:Delta Crystallin From Brucella Melitensis Bound to Cobalt within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Co471

b:10.0
occ:1.00
 OD2 B:ASP269 2.1 20.2 1.0
O B:HOH486 2.2 5.4 1.0
O B:HOH483 2.2 5.3 1.0
OE2 C:GLU209 2.2 18.9 1.0
OE2 B:GLU265 2.2 19.0 1.0
OE1 C:GLU209 2.3 20.3 1.0
CD C:GLU209 2.5 19.6 1.0
CD B:GLU265 2.9 20.1 1.0
OE1 B:GLU265 3.0 20.4 1.0
CG B:ASP269 3.2 22.0 1.0
O C:HOH477 3.5 22.8 1.0
CB B:ASP269 3.6 20.8 1.0
O B:HOH481 3.8 19.2 1.0
OG1 C:THR206 3.9 18.6 1.0
CG C:GLU209 4.0 20.5 1.0
OD1 B:ASP269 4.3 20.5 1.0
CG B:GLU265 4.4 19.4 1.0
NZ C:LYS286 4.6 19.0 1.0
CB C:GLU209 4.7 21.0 1.0
CB C:THR206 4.9 19.1 1.0
CA C:THR206 5.0 19.0 1.0

Cobalt binding site 5 out of 12 in 3oce

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Cobalt binding site 5 out of 12 in the Crystal Structure of Fumarate Lyase:Delta Crystallin From Brucella Melitensis Bound to Cobalt


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 Fumarate Lyase:Delta Crystallin From Brucella Melitensis Bound to Cobalt within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Co472

b:33.4
occ:1.00
 NE2 B:HIS40 2.0 35.6 1.0
O B:HOH497 2.0 29.6 1.0
O B:HOH499 2.2 16.6 1.0
O B:HOH498 2.3 17.5 1.0
O B:HOH500 2.4 12.4 1.0
CE1 B:HIS40 2.9 35.8 1.0
CD2 B:HIS40 3.0 33.3 1.0
ND1 B:HIS40 4.0 34.0 1.0
CG B:HIS40 4.1 30.3 1.0
OD1 B:ASN39 4.2 25.4 1.0
O B:ASP35 4.4 29.1 1.0
O D:HOH505 4.8 30.3 1.0

Cobalt binding site 6 out of 12 in 3oce

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Cobalt binding site 6 out of 12 in the Crystal Structure of Fumarate Lyase:Delta Crystallin From Brucella Melitensis Bound to Cobalt


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 Fumarate Lyase:Delta Crystallin From Brucella Melitensis Bound to Cobalt within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Co473

b:54.6
occ:1.00
 NE2 B:HIS164 2.3 31.2 1.0
CD2 B:HIS164 3.2 28.4 1.0
CE1 B:HIS164 3.3 29.6 1.0
CG B:HIS164 4.4 26.2 1.0
ND1 B:HIS164 4.4 28.2 1.0
OG1 B:THR211 4.7 20.4 1.0

Cobalt binding site 7 out of 12 in 3oce

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Cobalt binding site 7 out of 12 in the Crystal Structure of Fumarate Lyase:Delta Crystallin From Brucella Melitensis Bound to Cobalt


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 Fumarate Lyase:Delta Crystallin From Brucella Melitensis Bound to Cobalt within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Co471

b:14.9
occ:1.00
 OD2 C:ASP269 1.7 20.0 1.0
O C:HOH583 2.0 5.6 1.0
OE1 B:GLU209 2.1 18.9 1.0
OE2 C:GLU265 2.1 17.5 1.0
OE2 B:GLU209 2.2 17.4 1.0
CD B:GLU209 2.4 19.1 1.0
O B:HOH560 2.5 4.6 1.0
CG C:ASP269 2.8 22.5 1.0
CD C:GLU265 3.1 19.8 1.0
O C:HOH480 3.3 23.6 1.0
OE1 C:GLU265 3.3 20.6 1.0
CB C:ASP269 3.4 21.5 1.0
O C:HOH481 3.4 7.0 1.0
OD1 C:ASP269 3.8 22.8 1.0
CG B:GLU209 4.0 18.9 1.0
OG1 B:THR206 4.2 16.5 1.0
O C:HOH479 4.4 16.2 1.0
CG C:GLU265 4.5 20.4 1.0
O B:HOH496 4.6 13.7 1.0
NZ B:LYS286 4.7 16.4 1.0
CB B:GLU209 4.8 19.6 1.0
CA C:ASP269 4.9 21.1 1.0
O C:HOH492 4.9 7.2 1.0

Cobalt binding site 8 out of 12 in 3oce

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Cobalt binding site 8 out of 12 in the Crystal Structure of Fumarate Lyase:Delta Crystallin From Brucella Melitensis Bound to Cobalt


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 Fumarate Lyase:Delta Crystallin From Brucella Melitensis Bound to Cobalt within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Co472

b:33.5
occ:1.00
 NE2 C:HIS40 2.2 39.0 1.0
CD2 C:HIS40 3.1 35.8 1.0
CE1 C:HIS40 3.2 39.7 1.0
OD1 C:ASN39 4.2 28.7 1.0
CG C:HIS40 4.3 33.0 1.0
ND1 C:HIS40 4.3 36.6 1.0
O C:ASP35 4.4 30.0 1.0

Cobalt binding site 9 out of 12 in 3oce

Go back to Cobalt Binding Sites List in 3oce
Cobalt binding site 9 out of 12 in the Crystal Structure of Fumarate Lyase:Delta Crystallin From Brucella Melitensis Bound to Cobalt


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 Fumarate Lyase:Delta Crystallin From Brucella Melitensis Bound to Cobalt within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Co473

b:44.4
occ:1.00
 NE2 C:HIS164 2.4 35.5 1.0
CE1 C:HIS164 3.2 32.8 1.0
CD2 C:HIS164 3.3 32.4 1.0
ND1 C:HIS164 4.3 33.1 1.0
CG C:HIS164 4.4 29.7 1.0

Cobalt binding site 10 out of 12 in 3oce

Go back to Cobalt Binding Sites List in 3oce
Cobalt binding site 10 out of 12 in the Crystal Structure of Fumarate Lyase:Delta Crystallin From Brucella Melitensis Bound to Cobalt


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 Fumarate Lyase:Delta Crystallin From Brucella Melitensis Bound to Cobalt within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Co471

b:8.9
occ:1.00
 OE2 D:GLU265 2.1 23.4 1.0
OE1 A:GLU209 2.2 13.4 1.0
OD2 D:ASP269 2.2 17.9 1.0
O A:HOH492 2.2 4.4 1.0
OE2 A:GLU209 2.4 14.7 1.0
CD A:GLU209 2.6 15.6 1.0
CD D:GLU265 3.1 22.3 1.0
CG D:ASP269 3.2 19.7 1.0
OE1 D:GLU265 3.3 22.7 1.0
CB D:ASP269 3.5 18.8 1.0
O D:HOH504 3.7 10.9 1.0
O D:HOH564 3.7 36.6 1.0
O D:HOH502 3.8 24.4 1.0
OG1 A:THR206 4.1 14.0 1.0
CG A:GLU209 4.2 17.6 1.0
OD1 D:ASP269 4.3 17.4 1.0
CG D:GLU265 4.5 20.4 1.0
NZ A:LYS286 4.7 12.5 1.0
CA D:ASP269 4.9 19.2 1.0

Reference:

T.E.Edwards, T.L.Arakaki, B.Sankaran. Crystal Structure of Fumarate Lyase:Delta Crystallin From Brucella Melitensis Bound to Cobalt To Be Published.
Page generated: Tue Jul 30 16:22:39 2024

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