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Calcium in PDB 3ak5: Hemoglobin Protease (Hbp) Passenger Missing Domain-2

Protein crystallography data

The structure of Hemoglobin Protease (Hbp) Passenger Missing Domain-2, PDB code: 3ak5 was solved by K.Nishimura, S.-Y.Park, J.R.H.Tame, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.56 / 2.20
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 292.803, 53.936, 335.953, 90.00, 107.32, 90.00
R / Rfree (%) 22.6 / 28

Calcium Binding Sites:

The binding sites of Calcium atom in the Hemoglobin Protease (Hbp) Passenger Missing Domain-2 (pdb code 3ak5). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Hemoglobin Protease (Hbp) Passenger Missing Domain-2, PDB code: 3ak5:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 3ak5

Go back to Calcium Binding Sites List in 3ak5
Calcium binding site 1 out of 4 in the Hemoglobin Protease (Hbp) Passenger Missing Domain-2


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Hemoglobin Protease (Hbp) Passenger Missing Domain-2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1200

b:22.5
occ:1.00
OD2 A:ASP145 2.2 17.1 1.0
OE1 A:GLU306 2.2 22.9 1.0
OD1 A:ASN147 2.4 13.5 1.0
O A:HOH1201 2.5 23.2 1.0
O A:HOH49 2.5 15.5 1.0
O A:HOH1235 2.6 24.2 1.0
O A:HOH2 2.7 7.4 1.0
CD A:GLU306 3.3 25.5 1.0
CG A:ASP145 3.4 21.7 1.0
CG A:ASN147 3.6 14.8 1.0
CG A:GLU306 4.0 23.4 1.0
ND2 A:ASN147 4.1 11.5 1.0
OD2 A:ASP307 4.1 17.3 1.0
OE2 A:GLU306 4.2 26.2 1.0
CB A:ASP145 4.2 21.0 1.0
OD1 A:ASP145 4.3 19.2 1.0
O A:HOH553 4.4 28.2 1.0
O A:HOH9 4.4 9.7 1.0
OD1 A:ASP307 4.6 17.6 1.0
NZ A:LYS303 4.6 18.6 1.0
CD A:LYS303 4.6 20.3 1.0
ND2 A:ASN353 4.7 21.4 1.0
O A:HOH1281 4.8 27.2 1.0
CG A:ASP307 4.8 19.9 1.0
OD1 A:ASN353 4.8 18.1 1.0
CB A:ASN147 4.9 16.1 1.0
O A:HOH1195 5.0 22.6 1.0
O A:LYS303 5.0 22.7 1.0

Calcium binding site 2 out of 4 in 3ak5

Go back to Calcium Binding Sites List in 3ak5
Calcium binding site 2 out of 4 in the Hemoglobin Protease (Hbp) Passenger Missing Domain-2


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Hemoglobin Protease (Hbp) Passenger Missing Domain-2 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca1200

b:19.4
occ:1.00
OE2 B:GLU306 2.0 18.9 1.0
O B:HOH1160 2.2 20.8 1.0
OD2 B:ASP145 2.2 19.9 1.0
O B:HOH1272 2.5 26.6 1.0
O B:HOH8 2.5 9.6 1.0
OD1 B:ASN147 2.5 16.8 1.0
O B:HOH1248 2.9 22.8 1.0
CD B:GLU306 3.2 25.9 1.0
CG B:ASP145 3.3 20.1 1.0
CG B:ASN147 3.5 16.4 1.0
ND2 B:ASN147 3.9 12.8 1.0
CG B:GLU306 4.0 24.0 1.0
OD1 B:ASP145 4.0 18.7 1.0
OD2 B:ASP307 4.0 12.4 1.0
CB B:ASP145 4.1 19.4 1.0
OE1 B:GLU306 4.2 26.3 1.0
O B:HOH1127 4.6 18.8 1.0
NZ B:LYS303 4.6 19.5 1.0
ND2 B:ASN353 4.7 21.1 1.0
OD1 B:ASP307 4.8 16.1 1.0
CD B:LYS303 4.8 19.7 1.0
CB B:ASN147 4.8 15.8 1.0
CG B:ASP307 4.8 19.6 1.0
OD1 B:ASN353 4.8 16.4 1.0
O B:LYS303 4.9 22.5 1.0
O B:HOH19 5.0 12.3 1.0

Calcium binding site 3 out of 4 in 3ak5

Go back to Calcium Binding Sites List in 3ak5
Calcium binding site 3 out of 4 in the Hemoglobin Protease (Hbp) Passenger Missing Domain-2


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Hemoglobin Protease (Hbp) Passenger Missing Domain-2 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca1200

b:19.2
occ:1.00
OE1 C:GLU306 2.2 19.8 1.0
OD2 C:ASP145 2.3 16.8 1.0
O C:HOH1132 2.3 19.7 1.0
O C:HOH1115 2.4 18.1 1.0
O C:HOH38 2.6 14.3 1.0
OD1 C:ASN147 2.7 16.1 1.0
O C:HOH16 2.7 11.9 1.0
CG C:ASP145 3.3 21.3 1.0
CD C:GLU306 3.4 24.8 1.0
CG C:ASN147 3.7 17.7 1.0
OD2 C:ASP307 4.0 16.7 1.0
ND2 C:ASN147 4.0 12.0 1.0
OD1 C:ASP145 4.0 24.1 1.0
CB C:ASP145 4.1 20.5 1.0
CG C:GLU306 4.2 23.4 1.0
OE2 C:GLU306 4.3 25.4 1.0
ND2 C:ASN353 4.4 19.6 1.0
O C:HOH1302 4.4 32.8 1.0
NZ C:LYS303 4.5 18.2 1.0
O C:HOH1106 4.5 16.6 1.0
OD1 C:ASP307 4.6 20.2 1.0
CG C:ASP307 4.7 21.1 1.0
O C:HOH1103 4.7 16.9 1.0
OD1 C:ASN353 4.9 21.5 1.0
CB C:ASN147 5.0 18.3 1.0

Calcium binding site 4 out of 4 in 3ak5

Go back to Calcium Binding Sites List in 3ak5
Calcium binding site 4 out of 4 in the Hemoglobin Protease (Hbp) Passenger Missing Domain-2


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Hemoglobin Protease (Hbp) Passenger Missing Domain-2 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca1200

b:22.7
occ:1.00
OD2 D:ASP145 2.3 12.0 1.0
OE1 D:GLU306 2.3 21.7 1.0
O D:HOH12 2.3 10.7 1.0
OD1 D:ASN147 2.4 18.4 1.0
O D:HOH1174 2.4 24.2 1.0
O D:HOH46 2.4 15.3 1.0
O D:HOH1127 2.7 18.4 1.0
CG D:ASP145 3.4 21.1 1.0
CD D:GLU306 3.4 26.1 1.0
CG D:ASN147 3.5 19.3 1.0
ND2 D:ASN147 3.9 16.3 1.0
CG D:GLU306 4.1 19.6 1.0
OD1 D:ASP145 4.2 23.3 1.0
OD2 D:ASP307 4.2 16.8 1.0
CB D:ASP145 4.3 20.2 1.0
OE2 D:GLU306 4.4 27.0 1.0
O D:HOH1118 4.4 17.8 1.0
NZ D:LYS303 4.5 23.8 1.0
ND2 D:ASN353 4.6 23.1 1.0
CD D:LYS303 4.7 20.0 1.0
OD1 D:ASN353 4.7 17.4 1.0
OD1 D:ASP307 4.7 18.5 1.0
O D:HOH1316 4.8 40.2 1.0
CB D:ASN147 4.8 17.4 1.0
CG D:ASP307 4.9 19.1 1.0

Reference:

K.Nishimura, Y.-H.Yoon, A.Kurihara, S.Unzai, J.Luirink, S.-Y.Park, J.R.H.Tame. Role of Domains Within the Autotransporter Hbp/Tsh Acta Crystallogr.,Sect.D V. 66 1295 2010.
ISSN: ISSN 0907-4449
PubMed: 21123869
DOI: 10.1107/S0907444910036966
Page generated: Sat Dec 12 04:04:34 2020

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