Atomistry » Zinc » PDB 1iml-1jan » 1j2t
Atomistry »
  Zinc »
    PDB 1iml-1jan »
      1j2t »

Zinc in PDB 1j2t: Creatininase Mn

Enzymatic activity of Creatininase Mn

All present enzymatic activity of Creatininase Mn:
3.5.2.10;

Protein crystallography data

The structure of Creatininase Mn, PDB code: 1j2t was solved by T.Yoshimoto, N.Tanaka, N.Kanada, T.Inoue, Y.Nakajima, M.Haratake, K.T.Nakamura, Y.Xu, K.Ito, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 40.00 / 1.80
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 101.989, 150.742, 167.066, 90.00, 90.00, 90.00
R / Rfree (%) 17.5 / 19.3

Other elements in 1j2t:

The structure of Creatininase Mn also contains other interesting chemical elements:

Manganese (Mn) 6 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Creatininase Mn (pdb code 1j2t). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the Creatininase Mn, PDB code: 1j2t:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 1j2t

Go back to Zinc Binding Sites List in 1j2t
Zinc binding site 1 out of 6 in the Creatininase Mn


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Creatininase Mn within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn302

b:16.9
occ:1.00
 O A:HOH7008 1.9 14.4 1.0
OE1 A:GLU183 2.0 16.7 1.0
OD1 A:ASP45 2.0 14.6 1.0
NE2 A:HIS36 2.1 15.3 1.0
CD A:GLU183 2.7 14.9 1.0
OE2 A:GLU183 2.8 15.4 1.0
CG A:ASP45 3.0 14.5 1.0
CE1 A:HIS36 3.0 14.0 1.0
CD2 A:HIS36 3.1 15.9 1.0
OD2 A:ASP45 3.2 14.6 1.0
MN A:MN301 3.5 15.0 1.0
O A:HOH7010 3.8 20.9 1.0
ND1 A:HIS178 3.9 17.7 1.0
O A:HOH7011 3.9 17.9 1.0
OE2 A:GLU34 4.0 15.3 1.0
CG1 A:VAL44 4.1 15.6 1.0
CE1 A:HIS178 4.1 15.3 1.0
ND1 A:HIS36 4.1 14.7 1.0
CG A:GLU183 4.2 15.8 1.0
CG A:HIS36 4.2 15.6 1.0
CB A:ASP45 4.4 13.9 1.0
O A:GLY119 4.5 14.5 1.0
N A:ASP45 4.6 13.8 1.0
CB A:VAL44 4.6 14.9 1.0
CA A:ASP45 4.7 14.1 1.0
O A:HOH7009 4.8 17.3 1.0
O A:HOH7025 4.9 13.3 1.0

Zinc binding site 2 out of 6 in 1j2t

Go back to Zinc Binding Sites List in 1j2t
Zinc binding site 2 out of 6 in the Creatininase Mn


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Creatininase Mn within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn302

b:20.6
occ:1.00
 O B:HOH7009 1.9 17.6 1.0
OE1 B:GLU183 1.9 20.6 1.0
NE2 B:HIS36 2.0 19.3 1.0
OD1 B:ASP45 2.1 17.5 1.0
CD B:GLU183 2.7 21.1 1.0
OE2 B:GLU183 2.8 19.9 1.0
CE1 B:HIS36 2.9 16.6 1.0
CG B:ASP45 3.0 17.3 1.0
CD2 B:HIS36 3.1 18.1 1.0
OD2 B:ASP45 3.1 18.1 1.0
MN B:MN301 3.5 17.9 1.0
ND1 B:HIS178 3.7 22.0 1.0
CE1 B:HIS178 4.0 20.4 1.0
O B:HOH7012 4.0 18.3 1.0
O B:HOH7011 4.0 26.2 1.0
OE2 B:GLU34 4.0 17.6 1.0
ND1 B:HIS36 4.1 17.3 1.0
CG1 B:VAL44 4.1 18.2 1.0
CG B:GLU183 4.2 21.5 1.0
CG B:HIS36 4.2 18.8 1.0
CB B:ASP45 4.4 17.3 1.0
O B:GLY119 4.5 17.3 1.0
CB B:VAL44 4.6 17.4 1.0
N B:ASP45 4.6 17.4 1.0
CA B:ASP45 4.7 17.2 1.0
O B:HOH7010 4.9 19.2 1.0
O B:HOH7047 4.9 18.1 1.0

Zinc binding site 3 out of 6 in 1j2t

Go back to Zinc Binding Sites List in 1j2t
Zinc binding site 3 out of 6 in the Creatininase Mn


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Creatininase Mn within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn302

b:20.1
occ:1.00
 OE1 C:GLU183 1.9 19.9 1.0
O C:HOH7010 2.0 16.1 1.0
NE2 C:HIS36 2.0 17.0 1.0
OD1 C:ASP45 2.0 19.8 1.0
CD C:GLU183 2.7 18.0 1.0
OE2 C:GLU183 2.9 18.7 1.0
CE1 C:HIS36 2.9 17.4 1.0
CG C:ASP45 3.0 18.7 1.0
CD2 C:HIS36 3.1 18.2 1.0
OD2 C:ASP45 3.2 16.0 1.0
MN C:MN301 3.5 17.6 1.0
ND1 C:HIS178 3.7 19.2 1.0
CE1 C:HIS178 4.0 18.0 1.0
O C:HOH7013 4.0 20.6 1.0
ND1 C:HIS36 4.1 16.6 1.0
O C:HOH7012 4.1 29.7 1.0
OE2 C:GLU34 4.1 15.6 1.0
CG C:GLU183 4.2 19.2 1.0
CG C:HIS36 4.2 17.6 1.0
CG1 C:VAL44 4.2 17.5 1.0
CB C:ASP45 4.4 17.4 1.0
O C:GLY119 4.6 16.9 1.0
CB C:VAL44 4.6 16.9 1.0
O C:HOH7170 4.6 49.9 1.0
N C:ASP45 4.7 17.1 1.0
CA C:ASP45 4.7 17.1 1.0
O C:HOH7011 4.8 16.8 1.0
O C:HOH7017 5.0 15.6 1.0

Zinc binding site 4 out of 6 in 1j2t

Go back to Zinc Binding Sites List in 1j2t
Zinc binding site 4 out of 6 in the Creatininase Mn


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Creatininase Mn within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn302

b:21.1
occ:1.00
 OE1 D:GLU183 1.9 20.4 1.0
NE2 D:HIS36 2.0 20.1 1.0
OD1 D:ASP45 2.0 19.4 1.0
O D:HOH7002 2.0 19.7 1.0
CD D:GLU183 2.7 21.1 1.0
OE2 D:GLU183 2.8 20.2 1.0
CE1 D:HIS36 2.9 20.0 1.0
CG D:ASP45 3.0 19.8 1.0
CD2 D:HIS36 3.1 20.6 1.0
OD2 D:ASP45 3.2 19.5 1.0
MN D:MN301 3.5 18.8 1.0
O D:HOH7004 3.7 24.8 1.0
ND1 D:HIS178 3.8 17.5 1.0
O D:HOH7005 3.9 23.1 1.0
ND1 D:HIS36 4.1 19.9 1.0
CE1 D:HIS178 4.1 16.1 1.0
OE2 D:GLU34 4.1 18.2 1.0
CG D:GLU183 4.1 22.3 1.0
CG D:HIS36 4.2 20.0 1.0
CG1 D:VAL44 4.2 18.6 1.0
CB D:ASP45 4.3 18.3 1.0
O D:GLY119 4.5 17.2 1.0
CB D:VAL44 4.6 17.9 1.0
N D:ASP45 4.6 18.6 1.0
CA D:ASP45 4.7 18.6 1.0
O D:HOH7003 4.9 18.1 1.0
O D:HOH7014 5.0 19.9 1.0

Zinc binding site 5 out of 6 in 1j2t

Go back to Zinc Binding Sites List in 1j2t
Zinc binding site 5 out of 6 in the Creatininase Mn


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Creatininase Mn within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn302

b:20.8
occ:1.00
 OE1 E:GLU183 1.9 22.6 1.0
NE2 E:HIS36 2.0 19.5 1.0
OD1 E:ASP45 2.0 18.4 1.0
O E:HOH7004 2.1 18.8 1.0
CD E:GLU183 2.6 21.1 1.0
OE2 E:GLU183 2.7 19.1 1.0
CE1 E:HIS36 2.9 19.1 1.0
CG E:ASP45 3.0 18.1 1.0
CD2 E:HIS36 3.0 18.9 1.0
OD2 E:ASP45 3.1 17.4 1.0
MN E:MN301 3.5 18.2 1.0
O E:HOH7006 3.7 25.5 1.0
ND1 E:HIS178 3.8 19.4 1.0
O E:HOH7007 4.0 19.4 1.0
ND1 E:HIS36 4.0 18.8 1.0
CE1 E:HIS178 4.1 17.1 1.0
CG E:GLU183 4.1 22.6 1.0
CG E:HIS36 4.1 18.8 1.0
CG1 E:VAL44 4.2 19.2 1.0
OE2 E:GLU34 4.2 15.8 1.0
CB E:ASP45 4.4 18.2 1.0
O E:GLY119 4.5 17.3 1.0
N E:ASP45 4.6 18.4 1.0
CB E:VAL44 4.6 18.4 1.0
CA E:ASP45 4.7 18.3 1.0
O E:HOH7005 4.8 17.2 1.0
CB E:GLU183 4.9 21.9 1.0
O E:HOH7018 4.9 18.5 1.0

Zinc binding site 6 out of 6 in 1j2t

Go back to Zinc Binding Sites List in 1j2t
Zinc binding site 6 out of 6 in the Creatininase Mn


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Creatininase Mn within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn302

b:19.2
occ:1.00
 O F:HOH7011 1.9 15.7 1.0
OE1 F:GLU183 2.0 17.4 1.0
OD1 F:ASP45 2.0 14.9 1.0
NE2 F:HIS36 2.0 18.9 1.0
CD F:GLU183 2.7 18.0 1.0
OE2 F:GLU183 2.8 17.7 1.0
CG F:ASP45 3.0 15.2 1.0
CE1 F:HIS36 3.0 17.8 1.0
CD2 F:HIS36 3.0 18.2 1.0
OD2 F:ASP45 3.2 14.9 1.0
MN F:MN301 3.5 16.8 1.0
ND1 F:HIS178 3.8 17.6 1.0
O F:HOH7014 3.9 19.3 1.0
CE1 F:HIS178 4.0 17.8 1.0
O F:HOH7013 4.1 28.6 1.0
ND1 F:HIS36 4.1 17.4 1.0
CG1 F:VAL44 4.1 18.1 1.0
OE2 F:GLU34 4.1 16.8 1.0
CG F:HIS36 4.2 18.6 1.0
CG F:GLU183 4.2 17.2 1.0
CB F:ASP45 4.4 14.9 1.0
O F:HOH7189 4.4 45.3 1.0
O F:GLY119 4.5 15.7 1.0
CB F:VAL44 4.6 16.6 1.0
N F:ASP45 4.6 15.4 1.0
CA F:ASP45 4.7 15.0 1.0
O F:HOH7012 4.9 17.7 1.0
O F:HOH7026 5.0 15.6 1.0

Reference:

T.Yoshimoto, N.Tanaka, N.Kanada, T.Inoue, Y.Nakajima, M.Haratake, K.T.Nakamura, Y.Xu, K.Ito. Crystal Structures of Creatininase Reveal the Substrate Binding Site and Provide An Insight Into the Catalytic Mechanism J.Mol.Biol. V. 337 399 2004.
ISSN: ISSN 0022-2836
PubMed: 15003455
DOI: 10.1016/J.JMB.2004.01.022
Page generated: Sun Oct 13 03:17:58 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