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Calcium in PDB 1lvn: Crystal Structure of E. Coli Amine Oxidase Complexed with Tranylcypromine

Enzymatic activity of Crystal Structure of E. Coli Amine Oxidase Complexed with Tranylcypromine

All present enzymatic activity of Crystal Structure of E. Coli Amine Oxidase Complexed with Tranylcypromine:
1.4.3.6;

Protein crystallography data

The structure of Crystal Structure of E. Coli Amine Oxidase Complexed with Tranylcypromine, PDB code: 1lvn was solved by C.M.Wilmot, S.E.Phillips, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 2.40
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 135.236, 166.482, 79.628, 90.00, 90.00, 90.00
R / Rfree (%) 18.5 / 22.9

Other elements in 1lvn:

The structure of Crystal Structure of E. Coli Amine Oxidase Complexed with Tranylcypromine also contains other interesting chemical elements:

Copper (Cu) 2 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of E. Coli Amine Oxidase Complexed with Tranylcypromine (pdb code 1lvn). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Crystal Structure of E. Coli Amine Oxidase Complexed with Tranylcypromine, PDB code: 1lvn:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 1lvn

Go back to Calcium Binding Sites List in 1lvn
Calcium binding site 1 out of 4 in the Crystal Structure of E. Coli Amine Oxidase Complexed with Tranylcypromine


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of E. Coli Amine Oxidase Complexed with Tranylcypromine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca802

b:22.9
occ:1.00
 OD2 A:ASP678 2.3 20.2 1.0
OD2 A:ASP535 2.4 18.5 1.0
O A:ALA679 2.4 18.4 1.0
OD2 A:ASP533 2.4 23.2 1.0
O A:LEU534 2.4 20.6 1.0
O A:HOH1142 2.6 14.9 1.0
C A:LEU534 3.3 19.4 1.0
C A:ALA679 3.5 19.7 1.0
CG A:ASP678 3.6 22.9 1.0
CG A:ASP535 3.6 18.6 1.0
CG A:ASP533 3.6 21.9 1.0
N A:ALA679 3.6 18.7 1.0
NZ A:LYS133 3.7 19.6 1.0
C A:ASP533 4.0 20.2 1.0
N A:LEU534 4.0 20.4 1.0
N A:ASP535 4.0 18.2 1.0
CA A:ALA679 4.1 18.9 1.0
CA A:ASP535 4.2 17.4 1.0
O A:ASP533 4.2 19.9 1.0
C A:ASP678 4.3 20.9 1.0
CA A:LEU534 4.3 20.6 1.0
OD1 A:ASP678 4.3 23.9 1.0
OD1 A:ASP533 4.3 23.9 1.0
CA A:ASP533 4.4 18.8 1.0
OD1 A:ASP535 4.5 20.2 1.0
CA A:ASP678 4.5 20.9 1.0
CB A:ASP535 4.5 15.5 1.0
O A:GLU539 4.5 21.0 1.0
N A:VAL680 4.6 18.5 1.0
CB A:ASP678 4.6 20.6 1.0
CB A:ASP533 4.7 20.0 1.0
ND2 A:ASN541 4.7 19.6 1.0
CA A:VAL680 4.9 20.0 1.0

Calcium binding site 2 out of 4 in 1lvn

Go back to Calcium Binding Sites List in 1lvn
Calcium binding site 2 out of 4 in the Crystal Structure of E. Coli Amine Oxidase Complexed with Tranylcypromine


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of E. Coli Amine Oxidase Complexed with Tranylcypromine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca803

b:53.7
occ:1.00
 O A:TYR667 2.3 30.7 1.0
OE1 A:GLU573 2.7 24.7 1.0
O A:HOH1305 2.7 29.0 1.0
OE2 A:GLU672 2.8 40.2 1.0
OE2 A:GLU573 3.2 22.5 1.0
CD A:GLU573 3.3 25.6 1.0
C A:TYR667 3.5 30.9 1.0
OE1 A:GLU647 3.9 25.9 1.0
ND1 A:HIS644 3.9 51.9 1.0
CE1 A:HIS644 3.9 50.7 1.0
CD A:GLU672 4.0 41.6 1.0
OE2 A:GLU647 4.2 28.1 1.0
CA A:TYR667 4.3 30.2 1.0
N A:ARG642 4.3 22.0 1.0
CB A:THR641 4.3 23.1 1.0
CG A:GLU672 4.5 37.8 1.0
N A:SER668 4.5 32.8 1.0
CD A:GLU647 4.5 26.7 1.0
O A:ARG642 4.6 23.4 1.0
CB A:TYR667 4.7 30.6 1.0
CB A:ARG642 4.7 25.9 1.0
CA A:SER668 4.7 35.1 1.0
CG A:GLU573 4.7 27.3 1.0
CG2 A:THR641 4.8 19.7 1.0
OE1 A:GLU672 5.0 42.2 1.0
CA A:ARG642 5.0 24.2 1.0
CA A:THR641 5.0 23.3 1.0

Calcium binding site 3 out of 4 in 1lvn

Go back to Calcium Binding Sites List in 1lvn
Calcium binding site 3 out of 4 in the Crystal Structure of E. Coli Amine Oxidase Complexed with Tranylcypromine


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of E. Coli Amine Oxidase Complexed with Tranylcypromine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca802

b:24.6
occ:1.00
 O B:ALA679 2.3 29.4 1.0
OD2 B:ASP533 2.3 17.6 1.0
OD2 B:ASP535 2.4 21.0 1.0
OD2 B:ASP678 2.4 23.7 1.0
O B:HOH2151 2.5 18.8 1.0
O B:LEU534 2.5 28.7 1.0
C B:LEU534 3.3 25.6 1.0
C B:ALA679 3.4 27.9 1.0
CG B:ASP533 3.5 19.7 1.0
CG B:ASP678 3.6 27.2 1.0
CG B:ASP535 3.6 23.6 1.0
N B:ALA679 3.7 28.6 1.0
NZ B:LYS133 3.8 23.2 1.0
N B:LEU534 3.9 23.9 1.0
C B:ASP533 3.9 21.8 1.0
N B:ASP535 4.0 24.8 1.0
CA B:ALA679 4.1 27.9 1.0
C B:ASP678 4.2 29.3 1.0
CA B:ASP535 4.2 24.1 1.0
O B:ASP533 4.2 21.0 1.0
CA B:LEU534 4.2 25.8 1.0
OD1 B:ASP533 4.3 22.3 1.0
OD1 B:ASP678 4.3 25.9 1.0
CA B:ASP533 4.4 19.8 1.0
OD1 B:ASP535 4.5 22.8 1.0
CA B:ASP678 4.5 28.3 1.0
N B:VAL680 4.5 25.6 1.0
O B:GLU539 4.5 27.2 1.0
CB B:ASP535 4.5 24.0 1.0
CB B:ASP533 4.6 20.2 1.0
CB B:ASP678 4.7 27.1 1.0
ND2 B:ASN541 4.7 26.7 1.0
CG2 B:VAL680 4.8 21.6 1.0
CA B:VAL680 4.8 23.7 1.0
O B:ASP678 4.9 31.4 1.0
CB B:ALA679 4.9 28.8 1.0

Calcium binding site 4 out of 4 in 1lvn

Go back to Calcium Binding Sites List in 1lvn
Calcium binding site 4 out of 4 in the Crystal Structure of E. Coli Amine Oxidase Complexed with Tranylcypromine


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystal Structure of E. Coli Amine Oxidase Complexed with Tranylcypromine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca803

b:58.8
occ:1.00
 O B:TYR667 2.5 30.1 1.0
OE1 B:GLU573 2.5 39.2 1.0
OE2 B:GLU672 2.6 48.8 1.0
O B:HOH2176 2.6 63.7 1.0
OE2 B:GLU573 2.8 41.5 1.0
O B:HOH2180 2.9 39.0 1.0
CD B:GLU573 3.0 39.8 1.0
O B:HOH2230 3.1 59.6 1.0
CD B:GLU672 3.5 47.2 1.0
CG B:GLU672 3.6 45.2 1.0
C B:TYR667 3.7 31.3 1.0
NE2 B:HIS644 3.8 59.0 1.0
CD2 B:HIS644 4.0 58.4 1.0
CB B:GLU672 4.2 40.0 1.0
OE1 B:GLU647 4.4 30.7 1.0
O B:HOH2307 4.5 74.0 1.0
CG B:GLU573 4.5 38.5 1.0
CA B:SER668 4.6 35.7 1.0
N B:SER668 4.6 33.1 1.0
CA B:TYR667 4.6 30.3 1.0
N B:ARG642 4.6 31.8 1.0
OE1 B:GLU672 4.6 48.5 1.0
CG B:ARG642 4.7 37.1 1.0
CB B:THR641 4.8 28.1 1.0
OE2 B:GLU647 4.8 36.1 1.0
CB B:ARG642 4.9 34.8 1.0
CG2 B:THR641 4.9 28.1 1.0
CD B:ARG642 5.0 37.6 1.0

Reference:

C.M.Wilmot, C.G.Saysell, A.Blessington, D.A.Conn, C.R.Kurtis, M.J.Mcpherson, P.F.Knowles, S.E.Phillips. Medical Implications From the Crystal Structure of A Copper-Containing Amine Oxidase Complexed with the Antidepressant Drug Tranylcypromine. Febs Lett. V. 576 301 2004.
ISSN: ISSN 0014-5793
PubMed: 15498552
DOI: 10.1016/J.FEBSLET.2004.09.031
Page generated: Thu Jul 11 12:07:08 2024

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