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Cobalt in PDB 1xim: 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: 1xim 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 / 2.20
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 1xim). 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: 1xim:
Jump to Cobalt binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Cobalt binding site 1 out of 8 in 1xim

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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:33.2
occ:1.00
 OD2 A:ASP292 2.1 13.8 1.0
O2 A:XYL397 2.2 26.8 1.0
OD2 A:ASP245 2.2 17.3 1.0
OE2 A:GLU181 2.2 19.5 1.0
OE1 A:GLU217 2.2 18.9 1.0
O4 A:XYL397 2.5 28.2 1.0
CD A:GLU181 3.1 20.0 1.0
CG A:ASP292 3.2 13.1 1.0
OE1 A:GLU181 3.3 21.2 1.0
CG A:ASP245 3.3 16.6 1.0
C2 A:XYL397 3.4 28.3 1.0
CD A:GLU217 3.4 18.2 1.0
C4 A:XYL397 3.5 28.9 1.0
C3 A:XYL397 3.7 29.1 1.0
O3 A:XYL397 3.8 28.7 1.0
CB A:ASP245 3.9 14.2 1.0
CB A:ASP292 3.9 12.0 1.0
O A:HOH456 4.0 17.2 1.0
O A:HOH541 4.0 26.4 1.0
OD1 A:ASP292 4.1 13.5 1.0
CE1 A:HIS220 4.2 15.2 1.0
OE2 A:GLU217 4.2 18.9 1.0
CG A:GLU217 4.2 16.4 1.0
OD1 A:ASP245 4.3 17.7 1.0
CB A:GLU217 4.3 14.4 1.0
CG A:GLU181 4.4 18.0 1.0
C1 A:XYL397 4.5 28.7 1.0
NE2 A:HIS220 4.5 15.1 1.0
ND2 A:ASN215 4.7 10.4 1.0
C5 A:XYL397 4.8 28.1 1.0
CO A:CO396 4.8 28.8 0.5
O1 A:XYL397 4.8 29.8 1.0

Cobalt binding site 2 out of 8 in 1xim

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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:28.8
occ:0.50
 OE2 A:GLU217 2.2 18.9 1.0
O A:HOH541 2.3 26.4 1.0
OD1 A:ASP255 2.5 27.1 1.0
OD2 A:ASP255 2.5 32.9 1.0
O1 A:XYL397 2.7 29.8 1.0
NE2 A:HIS220 2.8 15.1 1.0
CG A:ASP255 2.9 27.6 1.0
OD1 A:ASP257 2.9 24.9 1.0
CD A:GLU217 3.2 18.2 1.0
CD2 A:HIS220 3.4 13.8 1.0
O2 A:XYL397 3.5 26.8 1.0
C1 A:XYL397 3.5 28.7 1.0
OE1 A:GLU217 3.5 18.9 1.0
CG A:ASP257 3.8 21.4 1.0
OD2 A:ASP257 3.8 22.6 1.0
CE1 A:HIS220 3.9 15.2 1.0
C2 A:XYL397 4.2 28.3 1.0
ND2 A:ASN247 4.3 11.2 1.0
CB A:ASP255 4.3 21.9 1.0
NZ A:LYS183 4.3 10.9 1.0
O A:HOH592 4.4 56.4 1.0
CE A:LYS183 4.5 8.5 1.0
CG A:GLU217 4.6 16.4 1.0
CG A:HIS220 4.7 13.6 1.0
O A:HOH429 4.8 24.2 1.0
CO A:CO395 4.8 33.2 1.0
ND1 A:HIS220 4.9 16.0 1.0

Cobalt binding site 3 out of 8 in 1xim

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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:39.1
occ:1.00
 OE1 B:GLU217 2.1 19.9 1.0
OD2 B:ASP245 2.2 17.3 1.0
OD2 B:ASP292 2.3 19.8 1.0
OE2 B:GLU181 2.3 22.2 1.0
O2 B:XYL397 2.3 31.6 1.0
O4 B:XYL397 2.5 30.2 1.0
CD B:GLU181 3.1 21.0 1.0
OE1 B:GLU181 3.1 21.2 1.0
CD B:GLU217 3.3 18.1 1.0
CG B:ASP292 3.4 18.3 1.0
CG B:ASP245 3.4 17.2 1.0
C2 B:XYL397 3.4 31.5 1.0
C4 B:XYL397 3.5 32.6 1.0
C3 B:XYL397 3.7 32.2 1.0
O3 B:XYL397 3.8 32.2 1.0
O B:HOH456 3.9 21.6 1.0
CB B:ASP292 4.0 15.8 1.0
CB B:ASP245 4.0 15.3 1.0
O B:HOH537 4.1 22.3 1.0
OE2 B:GLU217 4.1 20.1 1.0
CG B:GLU217 4.1 15.5 1.0
CE1 B:HIS220 4.1 17.4 1.0
CB B:GLU217 4.2 13.7 1.0
OD1 B:ASP245 4.3 16.9 1.0
OD1 B:ASP292 4.4 19.8 1.0
CG B:GLU181 4.5 19.0 1.0
NE2 B:HIS220 4.6 17.9 1.0
C1 B:XYL397 4.6 32.2 1.0
C5 B:XYL397 4.7 32.7 1.0
ND2 B:ASN215 4.8 19.0 1.0
O1 B:XYL397 4.8 30.7 1.0
CO B:CO396 4.9 23.8 0.5
ND1 B:HIS220 5.0 18.0 1.0

Cobalt binding site 4 out of 8 in 1xim

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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:23.8
occ:0.50
 O B:HOH537 2.3 22.3 1.0
OE2 B:GLU217 2.3 20.1 1.0
OD2 B:ASP255 2.4 31.8 1.0
OD1 B:ASP255 2.6 27.5 1.0
NE2 B:HIS220 2.7 17.9 1.0
O1 B:XYL397 2.7 30.7 1.0
CG B:ASP255 2.8 27.6 1.0
OD1 B:ASP257 2.9 23.4 1.0
CD B:GLU217 3.4 18.1 1.0
CD2 B:HIS220 3.4 15.9 1.0
O2 B:XYL397 3.6 31.6 1.0
OE1 B:GLU217 3.8 19.9 1.0
CE1 B:HIS220 3.8 17.4 1.0
OD2 B:ASP257 3.8 24.7 1.0
CG B:ASP257 3.8 21.2 1.0
C1 B:XYL397 3.9 32.2 1.0
NZ B:LYS183 4.1 12.4 1.0
ND2 B:ASN247 4.3 13.3 1.0
CB B:ASP255 4.3 22.0 1.0
O B:HOH429 4.4 22.9 1.0
C2 B:XYL397 4.4 31.5 1.0
CE B:LYS183 4.4 12.5 1.0
O B:HOH589 4.4 47.4 1.0
CG B:HIS220 4.7 16.0 1.0
CG B:GLU217 4.7 15.5 1.0
ND1 B:HIS220 4.8 18.0 1.0
CO B:CO395 4.9 39.1 1.0

Cobalt binding site 5 out of 8 in 1xim

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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:33.4
occ:1.00
 OD2 C:ASP245 2.2 19.0 1.0
OD2 C:ASP292 2.2 17.1 1.0
O2 C:XYL397 2.3 28.4 1.0
OE1 C:GLU217 2.3 19.2 1.0
OE2 C:GLU181 2.3 19.9 1.0
O4 C:XYL397 2.5 23.6 1.0
CD C:GLU181 3.1 17.9 1.0
CG C:ASP292 3.3 16.4 1.0
CG C:ASP245 3.4 16.1 1.0
OE1 C:GLU181 3.4 19.2 1.0
CD C:GLU217 3.5 18.6 1.0
C2 C:XYL397 3.5 28.4 1.0
C4 C:XYL397 3.6 25.5 1.0
C3 C:XYL397 3.8 27.2 1.0
O3 C:XYL397 3.8 26.6 1.0
CB C:ASP292 3.9 13.9 1.0
CB C:ASP245 3.9 14.0 1.0
O C:HOH467 4.0 17.6 1.0
O C:HOH552 4.1 24.5 1.0
CE1 C:HIS220 4.2 13.3 1.0
CG C:GLU217 4.3 15.8 1.0
OD1 C:ASP245 4.3 16.7 1.0
OE2 C:GLU217 4.3 19.3 1.0
CB C:GLU217 4.3 11.6 1.0
OD1 C:ASP292 4.3 17.5 1.0
CG C:GLU181 4.5 16.6 1.0
NE2 C:HIS220 4.5 13.7 1.0
C1 C:XYL397 4.6 30.6 1.0
ND2 C:ASN215 4.6 13.1 1.0
O1 C:XYL397 4.8 31.4 1.0
C5 C:XYL397 4.8 23.8 1.0
CO C:CO396 5.0 22.9 0.5

Cobalt binding site 6 out of 8 in 1xim

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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:22.9
occ:0.50
 O C:HOH552 2.3 24.5 1.0
OD2 C:ASP255 2.3 29.4 1.0
OE2 C:GLU217 2.3 19.3 1.0
OD1 C:ASP255 2.4 24.9 1.0
CG C:ASP255 2.7 25.6 1.0
NE2 C:HIS220 2.7 13.7 1.0
OD1 C:ASP257 2.8 23.0 1.0
O1 C:XYL397 3.0 31.4 1.0
CD C:GLU217 3.3 18.6 1.0
CD2 C:HIS220 3.3 12.5 1.0
OE1 C:GLU217 3.6 19.2 1.0
CG C:ASP257 3.7 21.4 1.0
OD2 C:ASP257 3.7 24.3 1.0
CE1 C:HIS220 3.9 13.3 1.0
O2 C:XYL397 3.9 28.4 1.0
C1 C:XYL397 4.0 30.6 1.0
CB C:ASP255 4.2 21.1 1.0
ND2 C:ASN247 4.2 11.3 1.0
O C:HOH438 4.3 27.1 1.0
NZ C:LYS183 4.4 11.1 1.0
CE C:LYS183 4.5 12.2 1.0
CG C:HIS220 4.6 11.8 1.0
O C:HOH610 4.6 54.3 1.0
CG C:GLU217 4.6 15.8 1.0
C2 C:XYL397 4.7 28.4 1.0
ND1 C:HIS220 4.8 13.5 1.0
CO C:CO395 5.0 33.4 1.0

Cobalt binding site 7 out of 8 in 1xim

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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:34.0
occ:1.00
 OD2 D:ASP292 2.1 15.3 1.0
OE1 D:GLU217 2.2 16.8 1.0
OE2 D:GLU181 2.2 22.3 1.0
OD2 D:ASP245 2.3 19.4 1.0
O2 D:XYL397 2.3 30.4 1.0
O4 D:XYL397 2.4 30.9 1.0
CD D:GLU181 3.2 20.3 1.0
CG D:ASP292 3.2 14.9 1.0
CG D:ASP245 3.4 18.4 1.0
C2 D:XYL397 3.4 30.5 1.0
CD D:GLU217 3.4 16.7 1.0
C4 D:XYL397 3.5 31.2 1.0
OE1 D:GLU181 3.5 20.9 1.0
O3 D:XYL397 3.6 32.4 1.0
C3 D:XYL397 3.6 31.4 1.0
CB D:ASP292 3.9 14.0 1.0
CB D:ASP245 3.9 15.4 1.0
O D:HOH548 3.9 26.2 1.0
O D:HOH467 4.0 20.7 1.0
CG D:GLU217 4.2 12.9 1.0
CE1 D:HIS220 4.2 13.5 1.0
OD1 D:ASP292 4.2 14.9 1.0
OE2 D:GLU217 4.2 16.6 1.0
CB D:GLU217 4.2 12.6 1.0
OD1 D:ASP245 4.4 18.3 1.0
CG D:GLU181 4.5 17.9 1.0
NE2 D:HIS220 4.5 14.9 1.0
C1 D:XYL397 4.6 30.5 1.0
CO D:CO396 4.7 10.8 0.5
C5 D:XYL397 4.7 30.5 1.0
ND2 D:ASN215 4.7 14.2 1.0
O1 D:XYL397 4.8 29.3 1.0
ND1 D:HIS220 5.0 13.2 1.0

Cobalt binding site 8 out of 8 in 1xim

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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:10.8
occ:0.50
 O D:HOH548 2.2 26.2 1.0
OD2 D:ASP255 2.3 28.2 1.0
OE2 D:GLU217 2.3 16.6 1.0
OD1 D:ASP255 2.6 24.6 1.0
OD1 D:ASP257 2.7 21.6 1.0
O1 D:XYL397 2.8 29.3 1.0
NE2 D:HIS220 2.8 14.9 1.0
CG D:ASP255 2.8 24.8 1.0
CD D:GLU217 3.2 16.7 1.0
O2 D:XYL397 3.3 30.4 1.0
OE1 D:GLU217 3.5 16.8 1.0
CG D:ASP257 3.6 20.1 1.0
CD2 D:HIS220 3.6 14.3 1.0
OD2 D:ASP257 3.6 23.9 1.0
C1 D:XYL397 3.7 30.5 1.0
CE1 D:HIS220 3.8 13.5 1.0
ND2 D:ASN247 4.2 9.7 1.0
C2 D:XYL397 4.3 30.5 1.0
CB D:ASP255 4.3 19.6 1.0
NZ D:LYS183 4.5 11.6 1.0
O D:HOH440 4.6 22.5 1.0
CG D:GLU217 4.6 12.9 1.0
CE D:LYS183 4.6 8.9 1.0
CO D:CO395 4.7 34.0 1.0
O D:HOH598 4.8 57.2 1.0
CG D:HIS220 4.8 12.5 1.0
OD2 D:ASP292 4.8 15.3 1.0
ND1 D:HIS220 4.9 13.2 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 14:46:27 2024

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