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Cobalt in PDB 6xm7: Crystal Structure of Dca-S Bound to Co-LSD4 From Sphingobium Sp. Strain Syk-6

Protein crystallography data

The structure of Crystal Structure of Dca-S Bound to Co-LSD4 From Sphingobium Sp. Strain Syk-6, PDB code: 6xm7 was solved by E.Kuatsjah, A.C.Chan, R.Katahira, G.T.Beckham, M.E.Murphy, L.D.Eltis, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 43.80 / 1.45
Space group I 2 2 2
Cell size a, b, c (Å), α, β, γ (°) 85.32, 112.02, 114.67, 90, 90, 90
R / Rfree (%) 13.4 / 15.4

Other elements in 6xm7:

The structure of Crystal Structure of Dca-S Bound to Co-LSD4 From Sphingobium Sp. Strain Syk-6 also contains other interesting chemical elements:

Magnesium (Mg) 1 atom

Cobalt Binding Sites:

The binding sites of Cobalt atom in the Crystal Structure of Dca-S Bound to Co-LSD4 From Sphingobium Sp. Strain Syk-6 (pdb code 6xm7). This binding sites where shown within 5.0 Angstroms radius around Cobalt atom.
In total 5 binding sites of Cobalt where determined in the Crystal Structure of Dca-S Bound to Co-LSD4 From Sphingobium Sp. Strain Syk-6, PDB code: 6xm7:
Jump to Cobalt binding site number: 1; 2; 3; 4; 5;

Cobalt binding site 1 out of 5 in 6xm7

Go back to Cobalt Binding Sites List in 6xm7
Cobalt binding site 1 out of 5 in the Crystal Structure of Dca-S Bound to Co-LSD4 From Sphingobium Sp. Strain Syk-6


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 Dca-S Bound to Co-LSD4 From Sphingobium Sp. Strain Syk-6 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Co510

b:15.0
occ:1.00
NE2 A:HIS218 2.0 14.8 1.0
NE2 A:HIS284 2.0 14.3 1.0
NE2 A:HIS476 2.0 12.6 1.0
NE2 A:HIS167 2.1 14.6 1.0
O A:HOH885 2.3 31.9 1.0
CE1 A:HIS476 2.9 14.2 1.0
CD2 A:HIS218 2.9 14.8 1.0
CE1 A:HIS167 3.0 12.9 1.0
CE1 A:HIS218 3.0 14.7 1.0
CD2 A:HIS284 3.0 14.1 1.0
CE1 A:HIS284 3.0 12.6 1.0
CD2 A:HIS476 3.0 14.1 1.0
HE1 A:HIS476 3.1 17.1 1.0
HE1 A:HIS167 3.1 15.5 1.0
CD2 A:HIS167 3.1 13.8 1.0
HD2 A:HIS218 3.1 17.8 1.0
HD2 A:HIS284 3.2 16.9 1.0
HE1 A:HIS218 3.2 17.6 1.0
HE1 A:HIS284 3.2 15.1 1.0
HD2 A:HIS476 3.3 16.9 1.0
HD2 A:HIS167 3.3 16.6 1.0
H101 A:V5M501 3.4 26.1 1.0
H061 A:V5M501 3.9 29.0 1.0
ND1 A:HIS476 4.0 12.9 1.0
ND1 A:HIS218 4.1 14.7 1.0
CG A:HIS218 4.1 13.1 1.0
CG A:HIS476 4.1 12.7 1.0
ND1 A:HIS284 4.1 14.3 1.0
ND1 A:HIS167 4.1 13.5 1.0
CG A:HIS284 4.1 14.0 1.0
O10 A:V5M501 4.2 21.8 1.0
CG A:HIS167 4.2 12.7 1.0
C06 A:V5M501 4.2 24.2 1.0
HG23 A:THR121 4.4 16.4 1.0
HG22 A:THR121 4.4 16.4 1.0
C07 A:V5M501 4.4 23.6 1.0
HG21 A:THR121 4.6 16.4 1.0
HB2 A:ASP219 4.6 15.8 1.0
CG2 A:THR121 4.7 13.7 1.0
C08 A:V5M501 4.8 24.4 1.0
C09 A:V5M501 4.8 24.8 1.0
HD1 A:HIS476 4.8 15.5 1.0
H071 A:V5M501 4.8 28.3 1.0
HD1 A:HIS218 4.8 17.6 1.0
HD12 A:LEU475 4.8 17.7 1.0
HD1 A:HIS167 4.9 16.2 1.0
HD1 A:HIS284 4.9 17.1 1.0
HE1 A:PHE354 4.9 28.1 1.0
C05 A:V5M501 5.0 20.5 1.0

Cobalt binding site 2 out of 5 in 6xm7

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Cobalt binding site 2 out of 5 in the Crystal Structure of Dca-S Bound to Co-LSD4 From Sphingobium Sp. Strain Syk-6


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 Dca-S Bound to Co-LSD4 From Sphingobium Sp. Strain Syk-6 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Co511

b:18.8
occ:0.46
HD1 A:HIS407 1.7 29.1 1.0
OE1 A:GLU373 2.0 30.4 1.0
OE2 A:GLU373 2.1 32.4 1.0
HG A:CYS394 2.1 23.6 0.5
CD A:GLU373 2.2 27.6 1.0
O A:HOH634 2.2 27.6 1.0
SG A:CYS394 2.2 20.8 0.5
ND1 A:HIS407 2.3 24.2 1.0
HB3 A:HIS407 2.4 24.6 1.0
HB3 A:CYS394 2.9 23.5 0.5
SG A:CYS394 3.0 19.7 0.5
CG A:HIS407 3.0 21.8 1.0
HB3 A:CYS394 3.1 23.2 0.5
CB A:HIS407 3.2 20.5 1.0
HB2 A:CYS394 3.2 23.5 0.5
CB A:CYS394 3.2 19.6 0.5
CB A:CYS394 3.2 19.4 0.5
HH21 A:ARG378 3.3 45.5 1.0
CE1 A:HIS407 3.4 24.8 1.0
HB2 A:CYS394 3.5 23.2 0.5
CG A:GLU373 3.5 30.5 1.0
HB2 A:ASP375 3.6 37.5 1.0
HG2 A:GLU373 3.7 36.6 1.0
HE1 A:HIS407 3.7 29.7 1.0
HB2 A:HIS407 3.8 24.6 1.0
HB3 A:GLU373 3.9 31.0 1.0
HA A:HIS407 4.0 23.4 1.0
NH2 A:ARG378 4.1 37.9 1.0
CA A:HIS407 4.2 19.5 1.0
OD2 A:ASP375 4.2 35.4 1.0
HG3 A:GLU373 4.2 36.6 1.0
CD2 A:HIS407 4.2 23.4 1.0
CB A:GLU373 4.3 25.8 1.0
O A:HOH1128 4.3 39.5 1.0
HE A:ARG378 4.3 43.3 1.0
NE2 A:HIS407 4.3 26.0 1.0
HB2 A:PHE396 4.4 23.9 1.0
CB A:ASP375 4.4 31.2 1.0
HH22 A:ARG378 4.5 45.5 1.0
HB2 A:GLU373 4.5 31.0 1.0
HG21 A:THR350 4.5 26.5 1.0
HD1 A:PHE396 4.6 27.1 1.0
CA A:CYS394 4.6 18.0 0.5
H A:TRP408 4.6 21.1 1.0
HG23 A:THR350 4.7 26.5 1.0
CA A:CYS394 4.7 17.7 0.5
HB3 A:ASP375 4.7 37.5 1.0
CG A:ASP375 4.7 35.7 1.0
O A:LEU395 4.8 15.8 1.0
C A:HIS407 4.9 19.1 1.0
N A:TRP408 4.9 17.5 1.0
HD2 A:HIS407 5.0 28.1 1.0
C A:CYS394 5.0 17.2 0.5
HA A:CYS394 5.0 21.6 0.5
NE A:ARG378 5.0 36.1 1.0

Cobalt binding site 3 out of 5 in 6xm7

Go back to Cobalt Binding Sites List in 6xm7
Cobalt binding site 3 out of 5 in the Crystal Structure of Dca-S Bound to Co-LSD4 From Sphingobium Sp. Strain Syk-6


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 Dca-S Bound to Co-LSD4 From Sphingobium Sp. Strain Syk-6 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Co512

b:18.1
occ:0.17
OD1 A:ASP448 2.0 18.6 1.0
O A:HOH862 2.0 23.6 1.0
O A:HOH682 2.0 23.8 0.5
ND1 A:HIS466 2.2 19.6 1.0
HB3 A:HIS466 3.0 18.5 1.0
HA A:HIS466 3.0 17.7 1.0
CG A:ASP448 3.0 16.4 1.0
CG A:HIS466 3.0 16.8 1.0
O A:HOH957 3.0 35.8 1.0
CE1 A:HIS466 3.1 20.4 1.0
CB A:HIS466 3.3 15.4 1.0
HE1 A:HIS466 3.3 24.5 1.0
OD2 A:ASP448 3.4 20.2 1.0
O A:HOH704 3.5 29.9 1.0
CA A:HIS466 3.6 14.7 1.0
O A:HOH1226 3.8 31.3 1.0
HG3 A:ARG441 3.8 21.0 1.0
O A:SER447 4.0 14.7 1.0
CD2 A:HIS466 4.1 20.3 1.0
H A:LEU467 4.1 16.5 1.0
NE2 A:HIS466 4.1 20.6 1.0
HA A:ASP448 4.2 17.0 1.0
HB2 A:HIS466 4.2 18.5 1.0
CB A:ASP448 4.3 15.3 1.0
C A:SER447 4.5 14.0 1.0
HB3 A:LYS446 4.5 18.4 1.0
N A:LEU467 4.5 13.7 1.0
C A:HIS466 4.5 14.1 1.0
HB2 A:LYS446 4.6 18.4 1.0
CA A:ASP448 4.6 14.2 1.0
CG A:ARG441 4.6 17.5 1.0
N A:HIS466 4.6 14.2 1.0
HG22 A:THR464 4.7 22.3 1.0
N A:ASP448 4.7 14.7 1.0
O A:LEU467 4.7 15.8 1.0
HG2 A:ARG441 4.7 21.0 1.0
HB3 A:ASP448 4.8 18.3 1.0
HE2 A:LYS446 4.8 21.2 1.0
HE A:ARG441 4.8 25.3 1.0
HD2 A:LYS446 4.9 19.9 1.0
HE2 A:HIS466 4.9 24.7 1.0
HB2 A:ASP448 4.9 18.3 1.0
HD2 A:HIS466 4.9 24.4 1.0
O A:VAL465 5.0 15.6 1.0
HB2 A:ARG441 5.0 20.9 1.0

Cobalt binding site 4 out of 5 in 6xm7

Go back to Cobalt Binding Sites List in 6xm7
Cobalt binding site 4 out of 5 in the Crystal Structure of Dca-S Bound to Co-LSD4 From Sphingobium Sp. Strain Syk-6


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 Dca-S Bound to Co-LSD4 From Sphingobium Sp. Strain Syk-6 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Co513

b:30.4
occ:0.30
O A:HOH1152 2.1 37.0 1.0
H A:ASN481 3.1 17.9 1.0
HG3 A:GLU484 3.5 30.6 1.0
ND2 A:ASN481 3.5 24.4 1.0
HA A:ALA480 3.6 15.8 1.0
HD21 A:ASN481 3.6 29.3 1.0
O A:HOH1215 3.7 32.0 1.0
HD22 A:ASN481 3.7 29.3 1.0
CG A:ASN481 3.8 19.3 1.0
HB2 A:ASN481 3.9 18.7 1.0
N A:ASN481 3.9 14.9 1.0
OD1 A:ASN481 4.2 18.0 1.0
HD1 A:TRP479 4.2 17.9 1.0
O A:HOH804 4.3 25.7 1.0
CB A:ASN481 4.3 15.6 1.0
CG A:GLU484 4.4 25.5 1.0
O A:HOH1013 4.5 31.2 1.0
CA A:ALA480 4.5 13.2 1.0
HG2 A:GLU484 4.5 30.6 1.0
O A:HOH720 4.6 20.9 1.0
O A:HOH747 4.6 27.4 1.0
O A:HOH1167 4.7 36.9 1.0
C A:ALA480 4.7 14.7 1.0
O A:TRP479 4.7 14.8 1.0
CA A:ASN481 4.8 14.3 1.0
O A:HOH1206 4.8 28.8 1.0
HD2 A:PRO423 4.8 21.3 1.0
O A:HOH1025 4.9 36.0 1.0
HB1 A:ALA480 4.9 19.8 1.0
CD1 A:TRP479 5.0 14.9 1.0
HE1 A:TRP479 5.0 17.6 1.0
HG2 A:PRO423 5.0 24.4 1.0

Cobalt binding site 5 out of 5 in 6xm7

Go back to Cobalt Binding Sites List in 6xm7
Cobalt binding site 5 out of 5 in the Crystal Structure of Dca-S Bound to Co-LSD4 From Sphingobium Sp. Strain Syk-6


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 Dca-S Bound to Co-LSD4 From Sphingobium Sp. Strain Syk-6 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Co514

b:38.4
occ:0.35
O A:HOH625 2.1 40.4 1.0
O A:DMS507 2.2 56.3 0.8
NE2 A:HIS314 2.3 27.3 1.0
CD2 A:HIS314 3.2 27.4 1.0
CE1 A:HIS314 3.3 26.0 1.0
HD2 A:HIS314 3.4 32.9 1.0
HE1 A:HIS314 3.4 31.2 1.0
S A:DMS507 3.7 55.3 0.8
OD2 A:ASP251 4.1 23.4 1.0
HG23 A:VAL313 4.2 28.3 1.0
H12 A:DMS507 4.2 63.9 0.8
H11 A:DMS507 4.3 63.9 0.8
C1 A:DMS507 4.3 53.3 0.8
ND1 A:HIS314 4.4 23.6 1.0
CG A:HIS314 4.4 25.9 1.0
HG1 A:THR253 4.5 27.0 1.0
O A:HOH627 4.6 45.5 1.0
HG21 A:VAL313 4.6 28.3 1.0
H22 A:DMS507 4.7 61.2 0.8
OG1 A:THR253 4.7 22.5 1.0
CG2 A:VAL313 4.9 23.6 1.0
CG A:ASP251 4.9 20.8 1.0
HG21 A:THR253 4.9 31.2 1.0
C2 A:DMS507 4.9 51.0 0.8
OD1 A:ASP251 4.9 22.5 1.0

Reference:

E.Kuatsjah, A.C.K.Chan, R.Katahira, S.J.Haugen, G.T.Beckham, M.E.Murphy, L.D.Eltis. Structural and Functional Analysis of Lignostilbene Dioxygenases From Sphingobium Sp. Syk-6 J.Biol.Chem. 2021.
ISSN: ESSN 1083-351X
Page generated: Sat Jul 10 13:30:28 2021

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