Atomistry » Cobalt » PDB 7w6v-7yvx » 7wsb
Atomistry »
  Cobalt »
    PDB 7w6v-7yvx »
      7wsb »

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

Go back to Cobalt Binding Sites List in 7wsb
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

Go back to Cobalt Binding Sites List in 7wsb
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

Go back to Cobalt Binding Sites List in 7wsb
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

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy