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Calcium in PDB 2yoc: Crystal Structure of Pula From Klebsiella Oxytoca

Enzymatic activity of Crystal Structure of Pula From Klebsiella Oxytoca

All present enzymatic activity of Crystal Structure of Pula From Klebsiella Oxytoca:
3.2.1.41;

Protein crystallography data

The structure of Crystal Structure of Pula From Klebsiella Oxytoca, PDB code: 2yoc was solved by O.Francetic, A.E.Mechaly, D.Tello-Manigne, A.Buschiazzo, C.Bernarde, N.Nadeau, A.P.Pugsley, P.M.Alzari, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 42.17 / 2.88
Space group P 63 2 2
Cell size a, b, c (Å), α, β, γ (°) 179.150, 179.150, 334.690, 90.00, 90.00, 120.00
R / Rfree (%) 17.11 / 21.31

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Pula From Klebsiella Oxytoca (pdb code 2yoc). 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 Pula From Klebsiella Oxytoca, PDB code: 2yoc:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Calcium binding site 1 out of 8 in 2yoc

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Calcium binding site 1 out of 8 in the Crystal Structure of Pula From Klebsiella Oxytoca


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 Pula From Klebsiella Oxytoca within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca2071

b:51.6
occ:1.00
 OD1 A:ASP469 2.3 63.4 1.0
OE1 A:GLU556 2.3 52.2 1.0
O A:LEU470 2.4 52.3 1.0
OE2 A:GLU475 2.7 62.7 1.0
O A:HOH3085 2.8 47.7 1.0
CD A:GLU556 3.1 69.8 1.0
CD A:GLU475 3.2 73.8 1.0
OE2 A:GLU556 3.3 81.9 1.0
CG A:ASP469 3.5 60.8 1.0
C A:LEU470 3.6 53.0 1.0
CG A:GLU475 3.7 57.0 1.0
OE1 A:GLU475 3.8 81.5 1.0
OG A:SER376 3.9 73.2 1.0
N A:LEU470 3.9 52.2 1.0
OD2 A:ASP469 4.2 60.5 1.0
CA A:LEU470 4.3 52.1 1.0
C A:ASP469 4.3 53.1 1.0
N A:GLY557 4.5 49.0 1.0
O A:VAL473 4.5 48.7 1.0
CB A:ASP469 4.6 46.7 1.0
CG A:GLU556 4.6 47.6 1.0
CA A:ASP469 4.6 45.8 1.0
N A:ALA471 4.6 48.9 1.0
CA A:GLU556 4.9 46.6 1.0
CA A:ALA471 4.9 48.8 1.0
CD2 A:PHE550 4.9 50.8 1.0
CG A:LEU470 4.9 61.1 1.0
OD1 A:ASN375 5.0 51.2 1.0

Calcium binding site 2 out of 8 in 2yoc

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Calcium binding site 2 out of 8 in the Crystal Structure of Pula From Klebsiella Oxytoca


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 Pula From Klebsiella Oxytoca within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca2072

b:0.3
occ:1.00
 OD1 A:ASP541 2.5 81.8 1.0
O A:TYR543 2.8 69.2 1.0
O A:ALA538 3.0 61.5 1.0
OD1 A:ASP881 3.2 0.0 1.0
OD2 A:ASP881 3.3 0.5 1.0
CG A:ASP881 3.6 99.1 1.0
O A:THR472 3.6 54.2 1.0
C A:TYR543 3.7 65.9 1.0
CG A:ASP541 3.8 82.3 1.0
O A:ASP541 3.9 62.5 1.0
C A:ALA538 4.2 63.6 1.0
N A:TYR543 4.3 59.0 1.0
C A:ASP541 4.3 66.0 1.0
CB A:ASN544 4.3 53.1 1.0
CG2 A:VAL473 4.3 51.9 1.0
CA A:TYR543 4.5 58.0 1.0
N A:ASN544 4.5 59.1 1.0
OD2 A:ASP541 4.5 93.6 1.0
N A:ASP541 4.6 64.4 1.0
ND2 A:ASN544 4.6 62.6 1.0
CA A:ASP541 4.7 63.8 1.0
CB A:ASP541 4.8 65.5 1.0
CA A:ASN544 4.8 57.0 1.0
C A:THR472 4.8 54.9 1.0
O A:HOH3086 4.9 51.7 1.0
C A:SER542 4.9 62.2 1.0
N A:SER542 5.0 62.4 1.0
CA A:ALA538 5.0 62.7 1.0

Calcium binding site 3 out of 8 in 2yoc

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Calcium binding site 3 out of 8 in the Crystal Structure of Pula From Klebsiella Oxytoca


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 Pula From Klebsiella Oxytoca within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca2073

b:0.3
occ:1.00
 O A:LEU994 2.2 0.2 1.0
OD2 A:ASP982 2.3 0.3 1.0
O A:ASP991 2.8 0.9 1.0
OE1 A:GLN1058 2.9 0.9 1.0
CG A:ASP982 3.2 0.1 1.0
OG A:SER989 3.2 0.9 1.0
C A:LEU994 3.3 0.3 1.0
CB A:SER989 3.6 0.6 1.0
O A:ASP982 3.6 0.2 1.0
CB A:ASP982 3.7 0.4 1.0
CD A:GLN1058 3.8 0.2 1.0
CA A:ASP995 3.9 0.7 1.0
N A:ASP995 4.0 0.9 1.0
OD1 A:ASP995 4.0 0.3 1.0
CA A:SER989 4.0 0.8 1.0
C A:ASP991 4.0 0.4 1.0
CG A:GLN1058 4.1 0.6 1.0
OD1 A:ASP982 4.2 0.4 1.0
C A:ASP982 4.4 0.9 1.0
CG A:GLN1062 4.4 0.2 1.0
N A:ASP991 4.5 0.8 1.0
CA A:LEU994 4.5 0.8 1.0
CB A:GLN1058 4.5 0.4 1.0
C A:SER989 4.6 1.0 1.0
CA A:ASP982 4.6 0.3 1.0
N A:LEU990 4.6 0.5 1.0
N A:LEU994 4.7 0.2 1.0
C A:ASP995 4.7 0.9 1.0
CA A:ASP991 4.8 0.3 1.0
CG A:ASP995 4.9 0.7 1.0
NE2 A:GLN1058 4.9 0.3 1.0
CB A:ASP995 4.9 0.1 1.0
N A:SER992 5.0 1.0 1.0

Calcium binding site 4 out of 8 in 2yoc

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Calcium binding site 4 out of 8 in the Crystal Structure of Pula From Klebsiella Oxytoca


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 Pula From Klebsiella Oxytoca within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca2074

b:0.3
occ:1.00
 NE A:ARG703 3.5 64.7 1.0
OD2 A:ASP702 3.5 67.5 1.0
OE2 A:GLU621 3.6 0.5 1.0
OE2 A:GLU627 3.8 80.1 1.0
OE1 A:GLU621 3.8 96.2 1.0
CD A:GLU621 4.1 0.6 1.0
OE1 A:GLU627 4.1 81.5 1.0
OE1 A:GLN700 4.1 69.1 1.0
NH2 A:ARG703 4.2 40.8 1.0
CZ A:ARG703 4.3 69.9 1.0
OD1 A:ASP702 4.3 78.7 1.0
CD A:ARG703 4.3 49.1 1.0
CG A:ASP702 4.3 72.3 1.0
CD A:GLU627 4.4 76.4 1.0
O A:ASN699 4.9 69.0 1.0

Calcium binding site 5 out of 8 in 2yoc

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Calcium binding site 5 out of 8 in the Crystal Structure of Pula From Klebsiella Oxytoca


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 Pula From Klebsiella Oxytoca within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca2075

b:58.0
occ:1.00
 OD1 B:ASP469 2.3 75.6 1.0
O B:LEU470 2.4 76.0 1.0
OE1 B:GLU556 2.5 58.8 1.0
OE2 B:GLU475 2.8 82.4 1.0
CD B:GLU475 3.1 89.3 1.0
CD B:GLU556 3.4 79.3 1.0
CG B:ASP469 3.5 76.5 1.0
OE2 B:GLU556 3.5 78.7 1.0
C B:LEU470 3.6 74.6 1.0
CG B:GLU475 3.7 76.7 1.0
OE1 B:GLU475 3.7 93.9 1.0
OG B:SER376 3.7 81.3 1.0
N B:LEU470 4.0 68.2 1.0
OD2 B:ASP469 4.2 82.8 1.0
CA B:LEU470 4.4 68.4 1.0
C B:ASP469 4.4 69.6 1.0
O B:VAL473 4.5 83.8 1.0
N B:ALA471 4.6 71.8 1.0
CB B:ASP469 4.6 69.5 1.0
CA B:ASP469 4.7 67.1 1.0
N B:GLY557 4.7 68.4 1.0
CD2 B:PHE550 4.7 65.6 1.0
OD1 B:ASN375 4.8 81.1 1.0
CA B:ALA471 4.8 73.5 1.0
CG B:GLU556 4.8 72.8 1.0

Calcium binding site 6 out of 8 in 2yoc

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Calcium binding site 6 out of 8 in the Crystal Structure of Pula From Klebsiella Oxytoca


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 Pula From Klebsiella Oxytoca within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca2076

b:0.3
occ:1.00
 OD1 B:ASP541 2.6 0.6 1.0
O B:ALA538 2.8 81.7 1.0
OD2 B:ASP881 3.0 0.3 1.0
O B:TYR543 3.1 85.2 1.0
OD1 B:ASP881 3.1 92.5 1.0
CG B:ASP881 3.4 95.8 1.0
O B:THR472 3.8 80.3 1.0
CG B:ASP541 3.9 0.0 1.0
C B:ALA538 4.0 81.5 1.0
C B:TYR543 4.0 82.5 1.0
O B:ASP541 4.1 85.5 1.0
C B:ASP541 4.5 85.5 1.0
CB B:ASN544 4.5 63.0 1.0
N B:ASP541 4.6 81.2 1.0
N B:TYR543 4.6 80.7 1.0
CG2 B:VAL473 4.6 74.4 1.0
OD2 B:ASP541 4.6 0.6 1.0
ND2 B:ASN544 4.7 73.4 1.0
C B:GLN539 4.8 78.2 1.0
N B:ASN544 4.8 74.8 1.0
CA B:ASP541 4.8 81.9 1.0
CA B:TYR543 4.8 79.2 1.0
O B:GLN539 4.8 77.5 1.0
CA B:ALA538 4.8 77.2 1.0
N B:GLN539 4.9 77.6 1.0
CB B:ASP541 4.9 84.3 1.0
CA B:GLN539 4.9 76.3 1.0
CB B:ASP881 5.0 88.1 1.0
C B:THR472 5.0 79.5 1.0

Calcium binding site 7 out of 8 in 2yoc

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Calcium binding site 7 out of 8 in the Crystal Structure of Pula From Klebsiella Oxytoca


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 Pula From Klebsiella Oxytoca within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca2077

b:78.8
occ:1.00
 OD2 B:ASP982 2.3 69.5 1.0
O B:LEU994 2.4 63.4 1.0
O B:ASP991 2.6 58.6 1.0
OE1 B:GLN1058 2.7 76.5 1.0
OG B:SER989 2.8 70.9 1.0
CG B:ASP982 3.2 61.5 1.0
CB B:SER989 3.3 54.6 1.0
C B:LEU994 3.6 65.2 1.0
CA B:SER989 3.7 52.0 1.0
CD B:GLN1058 3.7 80.8 1.0
C B:ASP991 3.8 57.7 1.0
O B:ASP982 3.8 51.9 1.0
CB B:ASP982 3.9 46.2 1.0
OD1 B:ASP982 4.1 61.6 1.0
C B:SER989 4.2 53.9 1.0
CG B:GLN1058 4.3 68.8 1.0
OD1 B:ASP995 4.3 73.9 1.0
N B:ASP991 4.3 51.5 1.0
CA B:ASP995 4.3 61.4 1.0
N B:ASP995 4.4 61.4 1.0
N B:LEU990 4.4 48.4 1.0
CG B:GLN1062 4.4 65.4 1.0
CA B:ASP991 4.6 52.3 1.0
C B:ASP982 4.6 50.3 1.0
N B:SER992 4.7 54.9 1.0
CB B:GLN1058 4.7 59.2 1.0
CA B:SER992 4.8 55.5 1.0
CA B:LEU994 4.8 62.7 1.0
NE2 B:GLN1058 4.8 75.9 1.0
N B:LEU994 4.8 63.1 1.0
CA B:ASP982 4.9 44.4 1.0
CB B:GLN1062 4.9 53.0 1.0
CB B:ASP991 5.0 54.8 1.0
C B:SER992 5.0 61.1 1.0
O B:SER989 5.0 56.5 1.0

Calcium binding site 8 out of 8 in 2yoc

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Calcium binding site 8 out of 8 in the Crystal Structure of Pula From Klebsiella Oxytoca


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 Pula From Klebsiella Oxytoca within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca2078

b:0.5
occ:1.00
 OD2 B:ASP702 3.0 83.7 1.0
O B:HOH3153 3.3 66.7 1.0
NE B:ARG703 3.5 72.1 1.0
OD1 B:ASP702 3.5 73.5 1.0
CG B:ASP702 3.7 73.9 1.0
OE1 B:GLN700 3.9 73.2 1.0
OE2 B:GLU621 4.0 0.4 1.0
CD B:ARG703 4.1 60.5 1.0
O B:ASN699 4.3 66.2 1.0
OE1 B:GLU621 4.5 72.2 1.0
CZ B:ARG703 4.5 79.0 1.0
OE2 B:GLU627 4.6 0.5 1.0
CD B:GLU621 4.6 91.4 1.0
OE1 B:GLU627 4.6 0.6 1.0
NH2 B:ARG703 4.6 64.3 1.0
CD B:GLN700 4.8 68.7 1.0
CG B:ARG703 4.8 50.8 1.0
NE2 B:GLN700 5.0 68.9 1.0

Reference:

O.Francetic, A.E.Mechaly, D.Tello-Manigne, A.Buschiazzo, C.Bernarde, N.Nadeau, A.P.Pugsley, P.M.Alzari. Crystal Structure of Pula From Klebsiella Oxytoca To Be Published.
Page generated: Tue Jul 8 09:42:50 2025

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