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Calcium in PDB 1n9e: Crystal Structure of Pichia Pastoris Lysyl Oxidase Pplo

Enzymatic activity of Crystal Structure of Pichia Pastoris Lysyl Oxidase Pplo

All present enzymatic activity of Crystal Structure of Pichia Pastoris Lysyl Oxidase Pplo:
1.4.3.13;

Protein crystallography data

The structure of Crystal Structure of Pichia Pastoris Lysyl Oxidase Pplo, PDB code: 1n9e was solved by J.M.Guss, A.P.Duff, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 24.60 / 1.65
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 248.442, 121.125, 151.841, 90.00, 124.64, 90.00
R / Rfree (%) 16.1 / 18.7

Other elements in 1n9e:

The structure of Crystal Structure of Pichia Pastoris Lysyl Oxidase Pplo also contains other interesting chemical elements:

Copper (Cu) 4 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Pichia Pastoris Lysyl Oxidase Pplo (pdb code 1n9e). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 8 binding sites of Calcium where determined in the Crystal Structure of Pichia Pastoris Lysyl Oxidase Pplo, PDB code: 1n9e:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Calcium binding site 1 out of 8 in 1n9e

Go back to Calcium Binding Sites List in 1n9e
Calcium binding site 1 out of 8 in the Crystal Structure of Pichia Pastoris Lysyl Oxidase Pplo


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 Pichia Pastoris Lysyl Oxidase Pplo within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca802

b:11.8
occ:1.00
 OD1 A:ASP537 2.3 11.2 1.0
OD1 A:ASP683 2.3 11.4 1.0
OD1 A:ASP539 2.3 14.9 1.0
O A:ILE684 2.4 12.1 1.0
O A:LEU538 2.4 10.7 1.0
O A:HOH2014 2.5 12.1 1.0
C A:LEU538 3.4 10.4 1.0
C A:ILE684 3.5 9.4 1.0
N A:ILE684 3.5 10.8 1.0
CG A:ASP537 3.5 13.2 1.0
CG A:ASP683 3.6 15.4 1.0
CG A:ASP539 3.6 11.8 1.0
NZ A:LYS105 3.7 12.5 1.0
C A:ASP537 4.0 10.2 1.0
N A:ASP539 4.1 10.1 1.0
CA A:ASP539 4.1 12.4 1.0
CA A:ILE684 4.1 11.5 1.0
C A:ASP683 4.2 12.5 1.0
OD2 A:ASP683 4.2 14.0 1.0
N A:LEU538 4.2 9.7 1.0
OD2 A:ASP537 4.2 13.3 1.0
O A:ASP537 4.2 11.0 1.0
OD2 A:ASP539 4.4 13.5 1.0
CA A:ASP537 4.4 9.8 1.0
CA A:ASP683 4.4 12.1 1.0
CB A:ASP539 4.4 10.5 1.0
CA A:LEU538 4.5 9.2 1.0
N A:VAL685 4.5 9.9 1.0
O A:THR543 4.6 15.6 1.0
CB A:ASP537 4.6 10.8 1.0
CB A:ASP683 4.6 12.1 1.0
OD1 A:ASN545 4.7 11.1 1.0
CG2 A:VAL685 4.8 12.1 1.0
CA A:VAL685 4.9 10.0 1.0
CB A:ILE684 4.9 11.3 1.0
O A:ASP683 5.0 11.7 1.0

Calcium binding site 2 out of 8 in 1n9e

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Calcium binding site 2 out of 8 in the Crystal Structure of Pichia Pastoris Lysyl Oxidase Pplo


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 Pichia Pastoris Lysyl Oxidase Pplo within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca803

b:13.1
occ:1.00
 OE1 A:GLU677 2.3 13.5 1.0
O A:HOH2066 2.3 13.8 1.0
O A:PHE673 2.4 13.4 1.0
OE2 A:GLU580 2.4 11.6 1.0
OD2 A:ASP675 2.4 14.1 1.0
O A:HOH2052 2.5 12.8 1.0
OE1 A:GLU580 2.5 13.6 1.0
CD A:GLU580 2.8 13.7 1.0
CD A:GLU677 3.3 22.5 1.0
CG A:ASP675 3.5 16.4 1.0
C A:PHE673 3.5 11.7 1.0
CG A:GLU677 3.8 11.9 1.0
OD1 A:ASP675 3.9 18.6 1.0
N A:ASP675 4.0 13.9 1.0
CB A:GLU677 4.2 13.2 1.0
NZ A:LYS648 4.2 14.4 1.0
OE2 A:GLU677 4.2 19.3 1.0
CG A:GLU580 4.3 10.9 1.0
OE1 A:GLU651 4.4 15.2 1.0
CA A:PHE673 4.4 12.4 1.0
CE A:LYS648 4.5 18.0 1.0
N A:LEU674 4.5 11.1 1.0
OE2 A:GLU651 4.5 14.9 1.0
CB A:ASP675 4.7 16.4 1.0
CA A:LEU674 4.7 11.2 1.0
N A:LYS646 4.7 12.3 1.0
CA A:ASP675 4.8 15.9 1.0
CB A:LYS646 4.8 14.2 1.0
C A:LEU674 4.8 12.7 1.0
CD A:GLU651 4.9 15.1 1.0
N A:GLU677 4.9 12.9 1.0
O A:LYS646 4.9 13.3 1.0
CB A:THR645 5.0 12.3 1.0

Calcium binding site 3 out of 8 in 1n9e

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Calcium binding site 3 out of 8 in the Crystal Structure of Pichia Pastoris Lysyl Oxidase Pplo


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 Pichia Pastoris Lysyl Oxidase Pplo within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca1802

b:8.6
occ:1.00
 OD1 B:ASP683 2.3 10.2 1.0
OD1 B:ASP537 2.3 8.8 1.0
O B:LEU538 2.3 9.2 1.0
OD1 B:ASP539 2.3 9.5 1.0
O B:ILE684 2.4 8.5 1.0
O B:HOH4014 2.4 9.2 1.0
C B:LEU538 3.4 8.6 1.0
C B:ILE684 3.5 9.6 1.0
CG B:ASP683 3.5 11.5 1.0
N B:ILE684 3.6 7.7 1.0
CG B:ASP537 3.6 9.3 1.0
CG B:ASP539 3.6 10.5 1.0
NZ B:LYS105 3.8 8.8 1.0
C B:ASP537 4.0 10.8 1.0
N B:ASP539 4.1 8.6 1.0
CA B:ASP539 4.1 8.5 1.0
CA B:ILE684 4.1 8.6 1.0
OD2 B:ASP683 4.2 14.0 1.0
C B:ASP683 4.2 7.9 1.0
N B:LEU538 4.2 10.4 1.0
OD2 B:ASP537 4.2 10.6 1.0
O B:ASP537 4.2 9.4 1.0
CA B:ASP537 4.4 7.7 1.0
CA B:ASP683 4.4 10.1 1.0
CA B:LEU538 4.4 8.7 1.0
OD2 B:ASP539 4.4 10.6 1.0
CB B:ASP539 4.4 9.9 1.0
N B:VAL685 4.5 8.2 1.0
CB B:ASP683 4.6 9.3 1.0
OD1 B:ASN545 4.6 10.4 1.0
O B:THR543 4.6 12.4 1.0
CB B:ASP537 4.6 8.7 1.0
CA B:VAL685 4.9 7.6 1.0
CG2 B:VAL685 4.9 10.4 1.0
CB B:ILE684 4.9 6.2 1.0

Calcium binding site 4 out of 8 in 1n9e

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Calcium binding site 4 out of 8 in the Crystal Structure of Pichia Pastoris Lysyl Oxidase Pplo


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 Pichia Pastoris Lysyl Oxidase Pplo within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca1803

b:10.0
occ:1.00
 OD2 B:ASP675 2.3 11.8 1.0
OE1 B:GLU677 2.3 11.1 1.0
O B:HOH4066 2.4 10.9 1.0
O B:PHE673 2.4 10.1 1.0
O B:HOH4052 2.4 11.5 1.0
OE2 B:GLU580 2.5 8.1 1.0
OE1 B:GLU580 2.5 9.3 1.0
CD B:GLU580 2.8 10.5 1.0
CD B:GLU677 3.3 15.0 1.0
CG B:ASP675 3.4 16.0 1.0
C B:PHE673 3.5 10.2 1.0
OD1 B:ASP675 3.9 17.5 1.0
CG B:GLU677 3.9 10.7 1.0
N B:ASP675 4.0 9.0 1.0
CB B:GLU677 4.2 12.6 1.0
NZ B:LYS648 4.2 11.2 1.0
OE2 B:GLU677 4.3 18.3 1.0
CA B:PHE673 4.3 10.3 1.0
OE1 B:GLU651 4.3 11.5 1.0
CG B:GLU580 4.3 10.8 1.0
OE2 B:GLU651 4.5 11.4 1.0
N B:LEU674 4.5 8.5 1.0
CE B:LYS648 4.5 11.7 1.0
CB B:ASP675 4.6 12.2 1.0
CA B:LEU674 4.7 9.7 1.0
N B:LYS646 4.7 9.4 1.0
CA B:ASP675 4.7 10.0 1.0
CB B:LYS646 4.8 9.1 1.0
CD B:GLU651 4.8 13.6 1.0
C B:LEU674 4.9 9.4 1.0
CB B:PHE673 4.9 10.7 1.0
N B:GLU677 4.9 11.1 1.0
CB B:THR645 5.0 10.6 1.0

Calcium binding site 5 out of 8 in 1n9e

Go back to Calcium Binding Sites List in 1n9e
Calcium binding site 5 out of 8 in the Crystal Structure of Pichia Pastoris Lysyl Oxidase Pplo


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Crystal Structure of Pichia Pastoris Lysyl Oxidase Pplo within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca3802

b:10.0
occ:1.00
 OD1 C:ASP537 2.3 9.8 1.0
OD1 C:ASP539 2.3 10.3 1.0
O C:LEU538 2.3 10.2 1.0
OD1 C:ASP683 2.4 10.6 1.0
O C:ILE684 2.4 8.3 1.0
O C:HOH6014 2.4 11.3 1.0
C C:LEU538 3.4 9.8 1.0
C C:ILE684 3.5 9.3 1.0
CG C:ASP537 3.5 9.9 1.0
CG C:ASP683 3.6 12.9 1.0
CG C:ASP539 3.6 11.6 1.0
N C:ILE684 3.6 9.8 1.0
NZ C:LYS105 3.8 10.1 1.0
C C:ASP537 4.0 12.2 1.0
CA C:ASP539 4.1 10.3 1.0
N C:ASP539 4.1 9.9 1.0
CA C:ILE684 4.1 9.2 1.0
N C:LEU538 4.2 9.7 1.0
OD2 C:ASP683 4.2 12.8 1.0
OD2 C:ASP537 4.2 12.0 1.0
C C:ASP683 4.2 10.2 1.0
O C:ASP537 4.2 11.8 1.0
CA C:ASP537 4.4 9.1 1.0
CA C:LEU538 4.4 11.2 1.0
OD2 C:ASP539 4.4 10.9 1.0
CA C:ASP683 4.4 9.1 1.0
CB C:ASP539 4.4 9.4 1.0
N C:VAL685 4.5 9.0 1.0
O C:THR543 4.5 14.7 1.0
CB C:ASP537 4.6 9.5 1.0
CB C:ASP683 4.6 9.2 1.0
OD1 C:ASN545 4.7 9.9 1.0
CA C:VAL685 4.9 8.9 1.0
CB C:ILE684 4.9 7.3 1.0

Calcium binding site 6 out of 8 in 1n9e

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Calcium binding site 6 out of 8 in the Crystal Structure of Pichia Pastoris Lysyl Oxidase Pplo


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Crystal Structure of Pichia Pastoris Lysyl Oxidase Pplo within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca3803

b:10.6
occ:1.00
 OE1 C:GLU677 2.3 10.0 1.0
OD2 C:ASP675 2.3 10.6 1.0
O C:PHE673 2.4 10.0 1.0
O C:HOH6066 2.4 11.0 1.0
O C:HOH6052 2.4 10.2 1.0
OE2 C:GLU580 2.5 10.7 1.0
OE1 C:GLU580 2.5 10.3 1.0
CD C:GLU580 2.8 10.0 1.0
CD C:GLU677 3.3 10.4 1.0
CG C:ASP675 3.4 15.1 1.0
C C:PHE673 3.5 10.6 1.0
OD1 C:ASP675 3.8 19.4 1.0
CG C:GLU677 3.9 11.3 1.0
N C:ASP675 4.0 10.8 1.0
CB C:GLU677 4.2 9.6 1.0
NZ C:LYS648 4.2 12.8 1.0
OE2 C:GLU677 4.2 16.4 1.0
CG C:GLU580 4.3 9.3 1.0
CA C:PHE673 4.3 9.4 1.0
OE1 C:GLU651 4.4 10.5 1.0
OE2 C:GLU651 4.5 11.5 1.0
N C:LEU674 4.5 8.3 1.0
CE C:LYS648 4.5 12.2 1.0
CB C:ASP675 4.6 10.2 1.0
CA C:LEU674 4.7 10.4 1.0
N C:LYS646 4.7 10.0 1.0
CA C:ASP675 4.7 8.9 1.0
CB C:LYS646 4.8 12.6 1.0
CD C:GLU651 4.9 12.4 1.0
N C:GLU677 4.9 12.1 1.0
C C:LEU674 4.9 11.2 1.0
CB C:PHE673 4.9 10.1 1.0

Calcium binding site 7 out of 8 in 1n9e

Go back to Calcium Binding Sites List in 1n9e
Calcium binding site 7 out of 8 in the Crystal Structure of Pichia Pastoris Lysyl Oxidase Pplo


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Crystal Structure of Pichia Pastoris Lysyl Oxidase Pplo within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca5802

b:12.2
occ:1.00
 OD1 D:ASP683 2.3 11.8 1.0
O D:LEU538 2.3 10.7 1.0
OD1 D:ASP537 2.3 12.7 1.0
OD1 D:ASP539 2.4 12.6 1.0
O D:ILE684 2.4 12.3 1.0
O D:HOH8014 2.4 11.9 1.0
C D:LEU538 3.4 11.2 1.0
C D:ILE684 3.4 10.8 1.0
CG D:ASP683 3.5 14.7 1.0
N D:ILE684 3.6 11.7 1.0
CG D:ASP537 3.6 12.9 1.0
CG D:ASP539 3.6 11.7 1.0
NZ D:LYS105 3.8 14.1 1.0
C D:ASP537 4.1 12.1 1.0
CA D:ILE684 4.1 12.0 1.0
N D:ASP539 4.1 10.0 1.0
CA D:ASP539 4.1 11.8 1.0
N D:LEU538 4.2 10.6 1.0
C D:ASP683 4.2 12.6 1.0
OD2 D:ASP683 4.2 13.7 1.0
OD2 D:ASP537 4.2 14.4 1.0
O D:ASP537 4.3 12.9 1.0
CA D:ASP683 4.4 12.3 1.0
OD2 D:ASP539 4.4 14.2 1.0
CA D:ASP537 4.4 12.1 1.0
CA D:LEU538 4.4 11.6 1.0
CB D:ASP539 4.5 11.0 1.0
N D:VAL685 4.5 11.3 1.0
O D:THR543 4.6 15.2 1.0
CB D:ASP683 4.6 11.6 1.0
OD1 D:ASN545 4.6 12.7 1.0
CB D:ASP537 4.6 10.7 1.0
CA D:VAL685 4.8 10.1 1.0
CB D:ILE684 4.9 10.3 1.0
CG2 D:VAL685 4.9 13.1 1.0
O D:ASP683 5.0 11.9 1.0

Calcium binding site 8 out of 8 in 1n9e

Go back to Calcium Binding Sites List in 1n9e
Calcium binding site 8 out of 8 in the Crystal Structure of Pichia Pastoris Lysyl Oxidase Pplo


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Crystal Structure of Pichia Pastoris Lysyl Oxidase Pplo within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca5803

b:14.0
occ:1.00
 O D:HOH8066 2.4 15.9 1.0
O D:PHE673 2.4 12.3 1.0
OE1 D:GLU677 2.4 13.3 1.0
OD2 D:ASP675 2.4 15.8 1.0
O D:HOH8052 2.4 14.3 1.0
OE2 D:GLU580 2.4 12.5 1.0
OE1 D:GLU580 2.5 14.7 1.0
CD D:GLU580 2.8 12.6 1.0
CD D:GLU677 3.3 19.8 1.0
CG D:ASP675 3.4 18.5 1.0
C D:PHE673 3.5 10.7 1.0
OD1 D:ASP675 3.8 20.1 1.0
CG D:GLU677 3.9 15.7 1.0
N D:ASP675 4.0 13.3 1.0
NZ D:LYS648 4.1 16.1 1.0
CB D:GLU677 4.2 14.5 1.0
OE2 D:GLU677 4.3 19.2 1.0
OE1 D:GLU651 4.3 14.8 1.0
CG D:GLU580 4.3 12.8 1.0
CA D:PHE673 4.4 11.9 1.0
N D:LEU674 4.4 12.0 1.0
CE D:LYS648 4.5 13.8 1.0
OE2 D:GLU651 4.5 16.1 1.0
CA D:LEU674 4.6 12.2 1.0
CB D:ASP675 4.7 15.4 1.0
N D:LYS646 4.7 12.3 1.0
CA D:ASP675 4.8 14.1 1.0
CB D:LYS646 4.8 11.3 1.0
C D:LEU674 4.8 12.4 1.0
CD D:GLU651 4.9 18.0 1.0
N D:GLU677 4.9 14.2 1.0
O D:LYS646 5.0 12.6 1.0
CB D:THR645 5.0 10.6 1.0

Reference:

A.P.Duff, A.E.Cohen, P.J.Ellis, J.A.Kuchar, D.B.Langley, E.M.Shepard, D.M.Dooley, H.C.Freeman, J.M.Guss. The Crystal Structure of Pichia Pastoris Lysyl Oxidase Biochemistry V. 42 15148 2003.
ISSN: ISSN 0006-2960
PubMed: 14690425
DOI: 10.1021/BI035338V
Page generated: Thu Jul 11 12:47:38 2024

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