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Cobalt in PDB 7wsb: The Ternary Complex Structure of FTMOX1 with A-Ketoglutarate and 13- Oxo-Fumitremorgin B

Enzymatic activity of The Ternary Complex Structure of FTMOX1 with A-Ketoglutarate and 13- Oxo-Fumitremorgin B

All present enzymatic activity of The Ternary Complex Structure of FTMOX1 with A-Ketoglutarate and 13- Oxo-Fumitremorgin B:
1.14.11.38;

Protein crystallography data

The structure of The Ternary Complex Structure of FTMOX1 with A-Ketoglutarate and 13- Oxo-Fumitremorgin B, PDB code: 7wsb was solved by J.Wang, X.Y.Wang, Y.Y.Wang, W.P.Yan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 2.87
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 104.05, 85.447, 160.768, 90, 108.84, 90
R / Rfree (%) 16.1 / 21.1

Cobalt Binding Sites:

The binding sites of Cobalt atom in the The Ternary Complex Structure of FTMOX1 with A-Ketoglutarate and 13- Oxo-Fumitremorgin B (pdb code 7wsb). This binding sites where shown within 5.0 Angstroms radius around Cobalt atom.
In total 6 binding sites of Cobalt where determined in the The Ternary Complex Structure of FTMOX1 with A-Ketoglutarate and 13- Oxo-Fumitremorgin B, PDB code: 7wsb:
Jump to Cobalt binding site number: 1; 2; 3; 4; 5; 6;

Cobalt binding site 1 out of 6 in 7wsb

Go back to Cobalt Binding Sites List in 7wsb
Cobalt binding site 1 out of 6 in the The Ternary Complex Structure of FTMOX1 with A-Ketoglutarate and 13- Oxo-Fumitremorgin B


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 1 of The Ternary Complex Structure of FTMOX1 with A-Ketoglutarate and 13- Oxo-Fumitremorgin B within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Co401

b:44.9
occ:1.00
 O2 A:AKG403 1.9 55.5 1.0
O A:HOH504 2.1 52.2 1.0
NE2 A:HIS129 2.1 47.0 1.0
NE2 A:HIS205 2.1 40.0 1.0
OD1 A:ASP131 2.3 44.9 1.0
O5 A:AKG403 2.3 55.0 1.0
C1 A:AKG403 2.7 61.0 1.0
C2 A:AKG403 2.8 48.9 1.0
CE1 A:HIS129 3.0 45.2 1.0
CD2 A:HIS205 3.1 42.3 1.0
CG A:ASP131 3.1 41.0 1.0
CE1 A:HIS205 3.1 42.0 1.0
CD2 A:HIS129 3.2 44.8 1.0
OD2 A:ASP131 3.2 40.4 1.0
OH A:TYR224 3.5 51.8 0.4
O1 A:AKG403 3.9 63.3 1.0
ND1 A:HIS129 4.1 50.7 1.0
CG A:HIS205 4.2 44.0 1.0
ND1 A:HIS205 4.2 40.3 1.0
CG A:HIS129 4.2 44.0 1.0
C3 A:AKG403 4.4 41.5 1.0
CZ A:TYR224 4.5 41.6 0.4
CB A:ASP131 4.5 39.4 1.0
C10 A:4IL402 4.7 52.1 0.8
N A:ASP131 4.9 44.2 1.0
CE1 A:TYR224 5.0 39.8 0.4
CA A:ASP131 5.0 45.8 1.0
C4 A:AKG403 5.0 48.8 1.0

Cobalt binding site 2 out of 6 in 7wsb

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Cobalt binding site 2 out of 6 in the The Ternary Complex Structure of FTMOX1 with A-Ketoglutarate and 13- Oxo-Fumitremorgin B


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 2 of The Ternary Complex Structure of FTMOX1 with A-Ketoglutarate and 13- Oxo-Fumitremorgin B within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Co401

b:28.5
occ:1.00
 NE2 B:HIS129 2.1 41.8 1.0
O1 B:AKG403 2.1 48.6 1.0
NE2 B:HIS205 2.2 31.1 1.0
O B:HOH501 2.2 38.6 1.0
O5 B:AKG403 2.2 46.3 1.0
OD1 B:ASP131 2.2 36.9 1.0
C1 B:AKG403 2.7 53.0 1.0
C2 B:AKG403 2.7 48.2 1.0
CD2 B:HIS205 2.9 35.2 1.0
CE1 B:HIS129 3.0 39.6 1.0
CD2 B:HIS129 3.1 38.3 1.0
CG B:ASP131 3.1 26.7 1.0
CE1 B:HIS205 3.3 33.2 1.0
OD2 B:ASP131 3.3 26.8 1.0
O2 B:AKG403 3.9 45.9 1.0
ND1 B:HIS129 4.1 35.3 1.0
CG B:HIS205 4.1 29.6 1.0
C3 B:AKG403 4.2 37.9 1.0
CG B:HIS129 4.2 30.5 1.0
ND1 B:HIS205 4.3 34.4 1.0
CB B:ASP131 4.5 26.5 1.0
C10 B:4IL402 4.8 43.0 0.9
CD2 B:LEU222 4.9 40.1 1.0
N B:ASP131 4.9 43.1 1.0
C14 B:4IL402 4.9 39.3 0.9
C4 B:AKG403 4.9 42.1 1.0
CA B:ASP131 4.9 26.7 1.0

Cobalt binding site 3 out of 6 in 7wsb

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Cobalt binding site 3 out of 6 in the The Ternary Complex Structure of FTMOX1 with A-Ketoglutarate and 13- Oxo-Fumitremorgin B


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 3 of The Ternary Complex Structure of FTMOX1 with A-Ketoglutarate and 13- Oxo-Fumitremorgin B within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Co401

b:43.6
occ:1.00
 O C:HOH505 2.0 45.7 1.0
O2 C:AKG403 2.0 57.6 1.0
NE2 C:HIS129 2.1 47.9 1.0
NE2 C:HIS205 2.2 39.7 1.0
OD1 C:ASP131 2.3 44.5 1.0
O5 C:AKG403 2.3 52.2 1.0
C1 C:AKG403 2.8 56.9 1.0
C2 C:AKG403 2.9 48.3 1.0
CE1 C:HIS129 3.0 43.0 1.0
CE1 C:HIS205 3.1 37.8 1.0
CD2 C:HIS129 3.1 47.8 1.0
CD2 C:HIS205 3.1 45.5 1.0
CG C:ASP131 3.2 44.7 1.0
OD2 C:ASP131 3.4 39.9 1.0
OH C:TYR224 3.6 55.0 0.4
O1 C:AKG403 4.0 65.6 1.0
ND1 C:HIS129 4.1 48.6 1.0
ND1 C:HIS205 4.2 37.3 1.0
CG C:HIS129 4.2 43.3 1.0
CG C:HIS205 4.2 41.3 1.0
C3 C:AKG403 4.4 42.0 1.0
CB C:ASP131 4.6 38.7 1.0
CZ C:TYR224 4.6 43.1 0.4
C10 C:4IL402 4.6 53.2 0.8
CD2 C:LEU222 4.8 66.4 1.0
CE1 C:TYR224 4.9 41.0 0.4
N C:ASP131 4.9 38.4 1.0
CA C:ASP131 5.0 40.2 1.0

Cobalt binding site 4 out of 6 in 7wsb

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Cobalt binding site 4 out of 6 in the The Ternary Complex Structure of FTMOX1 with A-Ketoglutarate and 13- Oxo-Fumitremorgin B


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 4 of The Ternary Complex Structure of FTMOX1 with A-Ketoglutarate and 13- Oxo-Fumitremorgin B within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Co401

b:33.0
occ:1.00
 O1 D:AKG403 2.0 42.5 1.0
NE2 D:HIS129 2.1 39.3 1.0
O D:HOH504 2.1 34.8 1.0
NE2 D:HIS205 2.2 33.0 1.0
OD1 D:ASP131 2.2 33.0 1.0
O5 D:AKG403 2.2 48.8 1.0
C1 D:AKG403 2.7 47.9 1.0
C2 D:AKG403 2.8 49.9 1.0
CD2 D:HIS205 2.9 34.5 1.0
CE1 D:HIS129 3.0 37.0 1.0
CD2 D:HIS129 3.1 38.5 1.0
CG D:ASP131 3.1 28.7 1.0
CE1 D:HIS205 3.3 34.3 1.0
OD2 D:ASP131 3.4 25.5 1.0
O2 D:AKG403 3.9 49.1 1.0
ND1 D:HIS129 4.1 37.2 1.0
CG D:HIS205 4.1 34.8 1.0
CG D:HIS129 4.2 30.3 1.0
C3 D:AKG403 4.3 42.7 1.0
ND1 D:HIS205 4.3 35.2 1.0
CB D:ASP131 4.5 31.3 1.0
C10 D:4IL402 4.7 38.9 0.9
N D:ASP131 4.8 38.2 1.0
CD2 D:LEU222 4.9 36.2 1.0
C4 D:AKG403 4.9 37.7 1.0
CA D:ASP131 4.9 25.3 1.0

Cobalt binding site 5 out of 6 in 7wsb

Go back to Cobalt Binding Sites List in 7wsb
Cobalt binding site 5 out of 6 in the The Ternary Complex Structure of FTMOX1 with A-Ketoglutarate and 13- Oxo-Fumitremorgin B


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 5 of The Ternary Complex Structure of FTMOX1 with A-Ketoglutarate and 13- Oxo-Fumitremorgin B within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Co401

b:57.8
occ:1.00
 O2 E:AKG403 1.9 72.8 1.0
NE2 E:HIS205 2.1 60.9 1.0
NE2 E:HIS129 2.2 61.7 1.0
O5 E:AKG403 2.2 70.4 1.0
O E:HOH502 2.2 70.6 1.0
OD1 E:ASP131 2.2 53.0 1.0
C1 E:AKG403 2.5 80.4 1.0
C2 E:AKG403 2.7 62.4 1.0
CE1 E:HIS205 3.0 59.0 1.0
CE1 E:HIS129 3.1 58.9 1.0
CD2 E:HIS205 3.1 60.7 1.0
CG E:ASP131 3.1 57.2 1.0
CD2 E:HIS129 3.2 60.2 1.0
OD2 E:ASP131 3.3 60.2 1.0
OH E:TYR224 3.6 59.6 0.4
O1 E:AKG403 3.6 86.2 1.0
ND1 E:HIS205 4.1 54.7 1.0
CG E:HIS205 4.2 55.8 1.0
ND1 E:HIS129 4.2 56.0 1.0
C3 E:AKG403 4.2 51.4 1.0
CG E:HIS129 4.2 54.7 1.0
CB E:ASP131 4.5 53.0 1.0
CZ E:TYR224 4.6 56.8 0.4
C4 E:AKG403 4.8 64.4 1.0
N E:ASP131 4.9 60.5 1.0
C10 E:4IL402 4.9 76.0 0.8
CA E:ASP131 4.9 50.9 1.0

Cobalt binding site 6 out of 6 in 7wsb

Go back to Cobalt Binding Sites List in 7wsb
Cobalt binding site 6 out of 6 in the The Ternary Complex Structure of FTMOX1 with A-Ketoglutarate and 13- Oxo-Fumitremorgin B


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 6 of The Ternary Complex Structure of FTMOX1 with A-Ketoglutarate and 13- Oxo-Fumitremorgin B within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Co401

b:62.1
occ:1.00
 O2 F:AKG403 2.0 70.4 1.0
NE2 F:HIS129 2.1 59.5 1.0
NE2 F:HIS205 2.2 67.2 1.0
OD1 F:ASP131 2.2 57.0 1.0
O F:HOH501 2.2 68.0 1.0
O5 F:AKG403 2.3 71.5 1.0
C1 F:AKG403 2.5 80.1 1.0
C2 F:AKG403 2.7 68.4 1.0
CE1 F:HIS129 2.9 60.8 1.0
CE1 F:HIS205 3.1 60.1 1.0
CG F:ASP131 3.1 56.3 1.0
CD2 F:HIS205 3.1 58.9 1.0
CD2 F:HIS129 3.1 60.0 1.0
OD2 F:ASP131 3.2 51.2 1.0
OH F:TYR224 3.3 59.4 0.5
O1 F:AKG403 3.6 87.6 1.0
ND1 F:HIS129 4.1 59.2 1.0
ND1 F:HIS205 4.1 59.2 1.0
CG F:HIS205 4.2 56.0 1.0
CG F:HIS129 4.2 58.6 1.0
C3 F:AKG403 4.2 49.3 1.0
CB F:ASP131 4.5 52.6 1.0
CZ F:TYR224 4.5 49.8 0.5
C4 F:AKG403 4.9 67.3 1.0
C10 F:4IL402 4.9 75.7 0.9
N F:ASP131 4.9 53.2 1.0
CA F:ASP131 4.9 56.8 1.0

Reference:

G.Zhu, W.Yan, X.Wang, R.Cheng, N.Naowarojna, K.Wang, J.Wang, H.Song, Y.Wang, H.Liu, X.Xia, C.E.Costello, X.Liu, L.Zhang, P.Liu. Dissecting the Mechanism of the Nonheme Iron Endoperoxidase FTMOX1 Using Substrate Analogues. Jacs Au V. 2 1686 2022.
ISSN: ESSN 2691-3704
PubMed: 35911443
DOI: 10.1021/JACSAU.2C00248
Page generated: Tue Jul 30 19:33:22 2024

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