Atomistry » Cobalt » PDB 3w72-4aq4 » 3xim
Atomistry »
  Cobalt »
    PDB 3w72-4aq4 »
      3xim »

Cobalt in PDB 3xim: Arginine Residues As Stabilizing Elements in Proteins

Enzymatic activity of Arginine Residues As Stabilizing Elements in Proteins

All present enzymatic activity of Arginine Residues As Stabilizing Elements in Proteins:
5.3.1.5;

Protein crystallography data

The structure of Arginine Residues As Stabilizing Elements in Proteins, PDB code: 3xim was solved by N.T.Mrabet, A.Van Denbroek, I.Van Den Brande, P.Stanssens, Y.Laroche, A.-M.Lambeir, G.Matthyssens, J.Jenkins, M.Chiadmi, H.Vantilbeurgh, F.Rey, J.Janin, W.J.Quax, I.Lasters, M.Demaeyer, S.J.Wodak, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) N/A / 2.30
Space group P 32 2 1
Cell size a, b, c (Å), α, β, γ (°) 143.450, 143.450, 231.500, 90.00, 90.00, 120.00
R / Rfree (%) n/a / n/a

Cobalt Binding Sites:

The binding sites of Cobalt atom in the Arginine Residues As Stabilizing Elements in Proteins (pdb code 3xim). This binding sites where shown within 5.0 Angstroms radius around Cobalt atom.
In total 8 binding sites of Cobalt where determined in the Arginine Residues As Stabilizing Elements in Proteins, PDB code: 3xim:
Jump to Cobalt binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Cobalt binding site 1 out of 8 in 3xim

Go back to Cobalt Binding Sites List in 3xim
Cobalt binding site 1 out of 8 in the Arginine Residues As Stabilizing Elements in Proteins


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 1 of Arginine Residues As Stabilizing Elements in Proteins within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Co395

b:17.5
occ:1.00
 OD2 A:ASP292 2.0 11.1 1.0
OD2 A:ASP245 2.1 13.3 1.0
OE1 A:GLU217 2.2 17.9 1.0
OE2 A:GLU181 2.2 11.8 1.0
O2 A:SOR397 2.2 22.0 1.0
O4 A:SOR397 2.4 22.5 1.0
CD A:GLU181 3.1 12.4 1.0
CG A:ASP292 3.1 9.8 1.0
CG A:ASP245 3.2 13.4 1.0
OE1 A:GLU181 3.3 11.4 1.0
C2 A:SOR397 3.3 22.1 1.0
CD A:GLU217 3.4 17.2 1.0
C4 A:SOR397 3.4 24.0 1.0
C3 A:SOR397 3.5 22.1 1.0
O3 A:SOR397 3.6 20.1 1.0
CB A:ASP292 3.7 8.3 1.0
CB A:ASP245 3.8 11.4 1.0
CO A:CO396 3.9 32.6 1.0
O A:HOH454 4.0 16.1 1.0
O A:HOH537 4.1 34.5 1.0
OE2 A:GLU217 4.1 19.8 1.0
OD1 A:ASP292 4.1 9.6 1.0
CG A:GLU217 4.2 15.8 1.0
OD1 A:ASP245 4.2 15.3 1.0
CE1 A:HIS220 4.2 14.6 1.0
CB A:GLU217 4.2 13.5 1.0
CG A:GLU181 4.4 9.8 1.0
NE2 A:HIS220 4.5 14.2 1.0
C1 A:SOR397 4.5 21.4 1.0
ND2 A:ASN215 4.7 7.6 1.0
C5 A:SOR397 4.8 24.8 1.0
O1 A:SOR397 5.0 21.3 1.0

Cobalt binding site 2 out of 8 in 3xim

Go back to Cobalt Binding Sites List in 3xim
Cobalt binding site 2 out of 8 in the Arginine Residues As Stabilizing Elements in Proteins


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 2 of Arginine Residues As Stabilizing Elements in Proteins within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Co396

b:32.6
occ:1.00
 OE2 A:GLU217 2.0 19.8 1.0
O A:HOH537 2.3 34.5 1.0
NE2 A:HIS220 2.4 14.2 1.0
OD1 A:ASP255 2.4 17.8 1.0
O2 A:SOR397 2.5 22.0 1.0
O1 A:SOR397 2.5 21.3 1.0
CD A:GLU217 2.8 17.2 1.0
OE1 A:GLU217 3.0 17.9 1.0
C1 A:SOR397 3.2 21.4 1.0
CE1 A:HIS220 3.2 14.6 1.0
OD1 A:ASP257 3.3 19.2 1.0
CD2 A:HIS220 3.3 12.6 1.0
C2 A:SOR397 3.4 22.1 1.0
CG A:ASP255 3.5 23.3 1.0
OD2 A:ASP255 3.6 27.6 1.0
CO A:CO395 3.9 17.5 1.0
OD2 A:ASP292 4.2 11.1 1.0
CG A:GLU217 4.2 15.8 1.0
CG A:ASP257 4.2 17.5 1.0
OD2 A:ASP257 4.3 20.3 1.0
ND1 A:HIS220 4.3 15.9 1.0
CG A:HIS220 4.4 13.4 1.0
ND2 A:ASN247 4.5 8.2 1.0
NZ A:LYS183 4.5 8.5 1.0
O3 A:SOR397 4.6 20.1 1.0
C3 A:SOR397 4.6 22.1 1.0
OE2 A:GLU181 4.6 11.8 1.0
CE A:LYS183 4.7 5.0 1.0
CG A:ASP292 4.7 9.8 1.0
OD1 A:ASP292 4.9 9.6 1.0
CB A:GLU217 4.9 13.5 1.0
CB A:ASP255 5.0 17.8 1.0

Cobalt binding site 3 out of 8 in 3xim

Go back to Cobalt Binding Sites List in 3xim
Cobalt binding site 3 out of 8 in the Arginine Residues As Stabilizing Elements in Proteins


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 3 of Arginine Residues As Stabilizing Elements in Proteins within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Co395

b:19.6
occ:1.00
 OE1 B:GLU217 2.1 18.4 1.0
OD2 B:ASP292 2.1 13.1 1.0
OD2 B:ASP245 2.1 14.1 1.0
OE2 B:GLU181 2.3 12.8 1.0
O4 B:SOR397 2.4 27.1 1.0
O2 B:SOR397 2.4 28.0 1.0
CD B:GLU181 3.0 14.9 1.0
OE1 B:GLU181 3.1 14.7 1.0
CG B:ASP292 3.2 13.9 1.0
CG B:ASP245 3.3 12.8 1.0
CD B:GLU217 3.3 15.1 1.0
C4 B:SOR397 3.4 28.3 1.0
C2 B:SOR397 3.4 26.8 1.0
C3 B:SOR397 3.6 26.6 1.0
O3 B:SOR397 3.6 25.5 1.0
CB B:ASP292 3.7 11.9 1.0
O B:HOH457 3.8 23.8 1.0
CB B:ASP245 3.8 11.9 1.0
CO B:CO396 3.9 35.2 1.0
OE2 B:GLU217 4.1 19.4 1.0
O B:HOH538 4.1 24.8 1.0
CG B:GLU217 4.2 13.8 1.0
CB B:GLU217 4.2 11.3 1.0
CE1 B:HIS220 4.2 13.9 1.0
OD1 B:ASP245 4.2 12.9 1.0
OD1 B:ASP292 4.3 15.1 1.0
CG B:GLU181 4.4 13.4 1.0
NE2 B:HIS220 4.7 15.5 1.0
C5 B:SOR397 4.7 28.4 1.0
C1 B:SOR397 4.7 26.6 1.0
ND2 B:ASN215 4.8 11.7 1.0
O6 B:SOR397 4.9 32.7 1.0

Cobalt binding site 4 out of 8 in 3xim

Go back to Cobalt Binding Sites List in 3xim
Cobalt binding site 4 out of 8 in the Arginine Residues As Stabilizing Elements in Proteins


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 4 of Arginine Residues As Stabilizing Elements in Proteins within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Co396

b:35.2
occ:1.00
 OE2 B:GLU217 2.2 19.4 1.0
O B:HOH538 2.3 24.8 1.0
NE2 B:HIS220 2.3 15.5 1.0
O2 B:SOR397 2.4 28.0 1.0
OD1 B:ASP255 2.7 22.9 1.0
O1 B:SOR397 2.8 24.1 1.0
CD B:GLU217 2.8 15.1 1.0
OE1 B:GLU217 3.1 18.4 1.0
CE1 B:HIS220 3.2 13.9 1.0
OD1 B:ASP257 3.3 19.1 1.0
CD2 B:HIS220 3.3 12.2 1.0
C1 B:SOR397 3.5 26.6 1.0
C2 B:SOR397 3.5 26.8 1.0
CG B:ASP255 3.7 24.3 1.0
OD2 B:ASP255 3.8 26.7 1.0
CO B:CO395 3.9 19.6 1.0
CG B:GLU217 4.2 13.8 1.0
OD2 B:ASP292 4.2 13.1 1.0
ND1 B:HIS220 4.3 14.4 1.0
CG B:ASP257 4.3 16.7 1.0
OD2 B:ASP257 4.3 20.3 1.0
ND2 B:ASN247 4.3 10.3 1.0
CG B:HIS220 4.3 13.3 1.0
NZ B:LYS183 4.4 11.2 1.0
O3 B:SOR397 4.6 25.5 1.0
OE2 B:GLU181 4.6 12.8 1.0
CE B:LYS183 4.6 9.5 1.0
C3 B:SOR397 4.7 26.6 1.0
CG B:ASP292 4.8 13.9 1.0
CD B:LYS183 4.8 9.9 1.0
CB B:GLU217 4.9 11.3 1.0

Cobalt binding site 5 out of 8 in 3xim

Go back to Cobalt Binding Sites List in 3xim
Cobalt binding site 5 out of 8 in the Arginine Residues As Stabilizing Elements in Proteins


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 5 of Arginine Residues As Stabilizing Elements in Proteins within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Co395

b:14.6
occ:1.00
 OD2 C:ASP292 2.0 11.5 1.0
OE1 C:GLU217 2.1 12.7 1.0
OD2 C:ASP245 2.1 14.5 1.0
OE2 C:GLU181 2.2 13.1 1.0
O4 C:SOR397 2.3 24.6 1.0
O2 C:SOR397 2.4 30.0 1.0
CD C:GLU181 3.1 14.2 1.0
CG C:ASP292 3.1 11.1 1.0
CG C:ASP245 3.2 13.0 1.0
OE1 C:GLU181 3.3 15.2 1.0
CD C:GLU217 3.3 12.7 1.0
C4 C:SOR397 3.3 25.1 1.0
C2 C:SOR397 3.5 27.5 1.0
CB C:ASP292 3.6 9.4 1.0
C3 C:SOR397 3.7 25.6 1.0
O3 C:SOR397 3.7 23.7 1.0
CB C:ASP245 3.8 11.4 1.0
O C:HOH472 3.9 20.1 1.0
O C:HOH553 4.1 28.7 1.0
CO C:CO396 4.1 36.3 1.0
CG C:GLU217 4.1 11.0 1.0
OD1 C:ASP292 4.2 10.2 1.0
OE2 C:GLU217 4.2 17.3 1.0
CE1 C:HIS220 4.2 11.4 1.0
CB C:GLU217 4.2 8.0 1.0
OD1 C:ASP245 4.2 14.6 1.0
CG C:GLU181 4.4 11.9 1.0
NE2 C:HIS220 4.6 10.8 1.0
ND2 C:ASN215 4.6 7.9 1.0
C5 C:SOR397 4.7 24.6 1.0
C1 C:SOR397 4.7 28.9 1.0
O6 C:SOR397 5.0 32.1 1.0

Cobalt binding site 6 out of 8 in 3xim

Go back to Cobalt Binding Sites List in 3xim
Cobalt binding site 6 out of 8 in the Arginine Residues As Stabilizing Elements in Proteins


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 6 of Arginine Residues As Stabilizing Elements in Proteins within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Co396

b:36.3
occ:1.00
 OE2 C:GLU217 2.2 17.3 1.0
O C:HOH553 2.2 28.7 1.0
NE2 C:HIS220 2.3 10.8 1.0
OD2 C:ASP255 2.5 27.1 1.0
O1 C:SOR397 2.8 27.7 1.0
O2 C:SOR397 2.8 30.0 1.0
CD C:GLU217 2.8 12.7 1.0
OD1 C:ASP257 3.0 19.5 1.0
OE1 C:GLU217 3.1 12.7 1.0
CD2 C:HIS220 3.2 9.7 1.0
CE1 C:HIS220 3.3 11.4 1.0
OD1 C:ASP255 3.5 33.3 1.0
C1 C:SOR397 3.5 28.9 1.0
CG C:ASP255 3.5 27.7 1.0
C2 C:SOR397 3.7 27.5 1.0
CG C:ASP257 4.0 17.0 1.0
O C:HOH618 4.0 58.8 1.0
OD2 C:ASP257 4.1 19.4 1.0
CO C:CO395 4.1 14.6 1.0
CG C:GLU217 4.3 11.0 1.0
CG C:HIS220 4.3 10.5 1.0
ND1 C:HIS220 4.3 12.1 1.0
ND2 C:ASN247 4.4 7.5 1.0
OD2 C:ASP292 4.5 11.5 1.0
NZ C:LYS183 4.6 8.5 1.0
CE C:LYS183 4.6 7.3 1.0
OE2 C:GLU181 4.7 13.1 1.0
O3 C:SOR397 4.8 23.7 1.0
CG C:ASP292 4.8 11.1 1.0
CB C:GLU217 4.9 8.0 1.0
C3 C:SOR397 4.9 25.6 1.0
CB C:ASP255 5.0 20.0 1.0

Cobalt binding site 7 out of 8 in 3xim

Go back to Cobalt Binding Sites List in 3xim
Cobalt binding site 7 out of 8 in the Arginine Residues As Stabilizing Elements in Proteins


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 7 of Arginine Residues As Stabilizing Elements in Proteins within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Co395

b:17.0
occ:1.00
 OE1 D:GLU217 2.0 12.6 1.0
OD2 D:ASP292 2.0 9.6 1.0
OE2 D:GLU181 2.1 13.6 1.0
OD2 D:ASP245 2.1 16.3 1.0
O4 D:SOR397 2.4 22.2 1.0
O2 D:SOR397 2.5 21.8 1.0
CD D:GLU181 3.0 14.6 1.0
CG D:ASP292 3.0 9.6 1.0
CG D:ASP245 3.2 15.2 1.0
CD D:GLU217 3.2 12.9 1.0
OE1 D:GLU181 3.3 15.8 1.0
O3 D:SOR397 3.5 20.2 1.0
C2 D:SOR397 3.5 20.2 1.0
C4 D:SOR397 3.5 22.3 1.0
CB D:ASP292 3.6 10.0 1.0
C3 D:SOR397 3.6 21.1 1.0
CB D:ASP245 3.7 12.9 1.0
O D:HOH470 3.8 20.8 1.0
CG D:GLU217 4.0 11.4 1.0
CO D:CO396 4.0 32.7 1.0
O D:HOH550 4.1 26.0 1.0
OE2 D:GLU217 4.1 17.9 1.0
OD1 D:ASP292 4.1 9.7 1.0
CB D:GLU217 4.2 10.6 1.0
OD1 D:ASP245 4.2 15.2 1.0
CE1 D:HIS220 4.2 8.5 1.0
CG D:GLU181 4.3 13.2 1.0
NE2 D:HIS220 4.6 9.3 1.0
C1 D:SOR397 4.7 19.3 1.0
ND2 D:ASN215 4.7 8.4 1.0
C5 D:SOR397 4.7 22.8 1.0

Cobalt binding site 8 out of 8 in 3xim

Go back to Cobalt Binding Sites List in 3xim
Cobalt binding site 8 out of 8 in the Arginine Residues As Stabilizing Elements in Proteins


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 8 of Arginine Residues As Stabilizing Elements in Proteins within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Co396

b:32.7
occ:1.00
 OE2 D:GLU217 2.1 17.9 1.0
NE2 D:HIS220 2.2 9.3 1.0
O D:HOH550 2.3 26.0 1.0
OD1 D:ASP255 2.3 22.2 1.0
O2 D:SOR397 2.5 21.8 1.0
O1 D:SOR397 2.6 16.5 1.0
CD D:GLU217 2.8 12.9 1.0
OE1 D:GLU217 3.0 12.6 1.0
CE1 D:HIS220 3.1 8.5 1.0
OD1 D:ASP257 3.1 19.2 1.0
CD2 D:HIS220 3.2 8.5 1.0
OD2 D:ASP255 3.3 25.2 1.0
CG D:ASP255 3.3 22.0 1.0
C1 D:SOR397 3.5 19.3 1.0
C2 D:SOR397 3.6 20.2 1.0
CG D:ASP257 4.0 18.1 1.0
CO D:CO395 4.0 17.0 1.0
OD2 D:ASP257 4.1 22.3 1.0
CG D:GLU217 4.2 11.4 1.0
ND1 D:HIS220 4.2 8.7 1.0
ND2 D:ASN247 4.3 4.0 1.0
CG D:HIS220 4.3 9.0 1.0
OD2 D:ASP292 4.3 9.6 1.0
CE D:LYS183 4.5 5.4 1.0
OE2 D:GLU181 4.7 13.6 1.0
O3 D:SOR397 4.7 20.2 1.0
NZ D:LYS183 4.7 8.4 1.0
C3 D:SOR397 4.8 21.1 1.0
CB D:ASP255 4.8 16.8 1.0
CG D:ASP292 4.8 9.6 1.0
CB D:GLU217 4.9 10.6 1.0

Reference:

N.T.Mrabet, A.Van Den Broeck, I.Van Den Brande, P.Stanssens, Y.Laroche, A.M.Lambeir, G.Matthijssens, J.Jenkins, M.Chiadmi, H.Van Tilbeurgh, F.Rey, J.Janin, W.J.Quax, I.Lasters, M.Demaeyer, S.J.Wodak. Arginine Residues As Stabilizing Elements in Proteins. Biochemistry V. 31 2239 1992.
ISSN: ISSN 0006-2960
PubMed: 1540579
DOI: 10.1021/BI00123A005
Page generated: Tue Jul 30 16:55:40 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