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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: Wed Dec 16 02:53:14 2020

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