Calcium in PDB 9etj: Mouse Cnpase Catalytic Domain with Nanobody 10E

Enzymatic activity of Mouse Cnpase Catalytic Domain with Nanobody 10E

All present enzymatic activity of Mouse Cnpase Catalytic Domain with Nanobody 10E:
3.1.4.37;

Protein crystallography data

The structure of Mouse Cnpase Catalytic Domain with Nanobody 10E, PDB code: 9etj was solved by S.Markusson, A.Raasakka, F.Opazo, P.Kursula, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.95 / 2.55
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 101.73, 118.25, 122.45, 90, 90, 90
R / Rfree (%) 25.2 / 30.4

Calcium Binding Sites:

The binding sites of Calcium atom in the Mouse Cnpase Catalytic Domain with Nanobody 10E (pdb code 9etj). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 7 binding sites of Calcium where determined in the Mouse Cnpase Catalytic Domain with Nanobody 10E, PDB code: 9etj:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7;

Calcium binding site 1 out of 7 in 9etj

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Calcium binding site 1 out of 7 in the Mouse Cnpase Catalytic Domain with Nanobody 10E


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Mouse Cnpase Catalytic Domain with Nanobody 10E within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca201

b:88.4
occ:1.00
O C:PRO114 2.4 75.4 1.0
OD2 C:ASP98 2.6 76.1 1.0
OD1 C:ASP116 2.6 70.7 1.0
OD1 C:ASP96 2.7 69.8 1.0
OD1 A:ASP237 2.9 79.5 1.0
HE2 A:TYR238 3.5 94.6 1.0
HB2 C:ASP98 3.5 86.8 1.0
C C:PRO114 3.5 74.5 1.0
CG C:ASP98 3.7 73.1 1.0
CG C:ASP116 3.7 70.6 1.0
CG C:ASP96 3.7 69.5 1.0
HB3 C:PRO114 3.8 89.1 1.0
CG A:ASP237 3.9 81.8 1.0
HA C:PRO114 3.9 92.0 1.0
H C:ASP98 4.0 86.4 1.0
OD2 C:ASP96 4.0 67.4 1.0
OD2 C:ASP116 4.1 70.9 1.0
CB C:ASP98 4.1 71.5 1.0
CA C:PRO114 4.1 75.8 1.0
HD2 A:TYR238 4.2 95.7 1.0
OD2 A:ASP237 4.2 82.6 1.0
HA C:TYR115 4.3 87.9 1.0
CE2 A:TYR238 4.3 77.9 1.0
CB C:PRO114 4.3 73.3 1.0
HB2 C:PRO114 4.5 89.1 1.0
O C:TYR115 4.5 75.5 1.0
HE2 A:LYS240 4.6 113.5 1.0
HH12 C:ARG102 4.6 83.2 1.0
N C:TYR115 4.6 72.7 1.0
C C:TYR115 4.6 73.8 1.0
CD2 A:TYR238 4.7 78.8 1.0
N C:ASP98 4.7 71.1 1.0
HD3 C:ARG102 4.7 81.4 1.0
HD11 A:LEU167 4.7 88.2 1.0
HA C:ASP96 4.7 82.4 1.0
CA C:TYR115 4.7 72.4 1.0
HE3 A:LYS240 4.8 113.5 1.0
HD13 A:LEU167 4.8 88.2 1.0
H C:ASN97 4.8 84.5 1.0
HB3 C:ASP98 4.8 86.8 1.0
OD1 C:ASP98 4.8 75.8 1.0
HD2 C:ARG102 4.9 81.4 1.0
N C:ASP116 5.0 73.0 1.0
CB C:ASP96 5.0 67.0 1.0

Calcium binding site 2 out of 7 in 9etj

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Calcium binding site 2 out of 7 in the Mouse Cnpase Catalytic Domain with Nanobody 10E


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Mouse Cnpase Catalytic Domain with Nanobody 10E within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca202

b:73.8
occ:1.00
OD1 C:ASN97 2.3 68.9 1.0
O C:ASN97 2.5 68.8 1.0
O C:ASP31 2.6 74.4 1.0
CG C:ASN97 3.5 70.3 1.0
C C:ASN97 3.5 66.3 1.0
HA C:ASN97 3.6 85.3 1.0
O C:LEU99 3.8 68.7 1.0
C C:ASP31 3.8 78.1 1.0
HA C:ASP31 4.0 94.8 1.0
CA C:ASN97 4.1 70.1 1.0
OD2 C:ASP101 4.1 68.2 1.0
HG3 C:PRO53 4.2 93.6 1.0
HB3 C:ASP31 4.3 92.2 1.0
CB C:ASN97 4.4 69.8 1.0
HA C:PHE32 4.4 93.9 1.0
HA C:ASP98 4.4 81.2 1.0
CA C:ASP31 4.4 78.1 1.0
ND2 C:ASN97 4.5 69.7 1.0
HD22 C:ASN97 4.5 84.7 1.0
N C:ASP98 4.7 71.1 1.0
HG2 C:PRO53 4.7 93.6 1.0
H C:LEU99 4.8 92.1 1.0
HB3 C:ASN97 4.8 84.9 1.0
CB C:ASP31 4.9 75.9 1.0
C C:LEU99 4.9 66.1 1.0
N C:PHE32 4.9 77.7 1.0
CG C:PRO53 4.9 77.1 1.0
HD2 C:PRO100 5.0 83.4 1.0
CA C:ASP98 5.0 66.7 1.0

Calcium binding site 3 out of 7 in 9etj

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Calcium binding site 3 out of 7 in the Mouse Cnpase Catalytic Domain with Nanobody 10E


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Mouse Cnpase Catalytic Domain with Nanobody 10E within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca201

b:80.3
occ:1.00
O D:PRO114 2.5 78.1 1.0
OD1 B:ASP237 2.6 86.2 1.0
OD2 D:ASP98 2.7 76.3 1.0
OD1 D:ASP116 2.8 72.9 1.0
HE2 B:TYR238 3.3 98.7 1.0
OD1 D:ASP96 3.3 70.3 1.0
HZ3 B:LYS240 3.4 120.7 1.0
CG B:ASP237 3.5 87.0 1.0
C D:PRO114 3.6 76.1 1.0
HA D:PRO114 3.7 93.0 1.0
HB3 D:PRO114 3.7 91.4 1.0
HD2 B:TYR238 3.8 101.2 1.0
CG D:ASP98 3.8 75.3 1.0
HB2 D:ASP98 3.8 88.4 1.0
OD2 B:ASP237 3.8 88.3 1.0
HZ1 B:LYS240 3.9 120.7 1.0
CG D:ASP116 3.9 72.0 1.0
NZ B:LYS240 4.0 99.6 1.0
CE2 B:TYR238 4.0 81.3 1.0
CA D:PRO114 4.0 76.6 1.0
HZ2 B:LYS240 4.2 120.7 1.0
CG D:ASP96 4.3 70.5 1.0
CB D:PRO114 4.3 75.2 1.0
OD2 D:ASP116 4.3 74.7 1.0
CD2 B:TYR238 4.3 83.5 1.0
CB D:ASP98 4.4 72.8 1.0
HB2 D:PRO114 4.4 91.4 1.0
OD2 D:ASP96 4.5 71.5 1.0
H D:ASP98 4.5 86.4 1.0
HA D:TYR115 4.5 90.3 1.0
HD11 B:LEU167 4.6 91.4 1.0
N D:TYR115 4.7 75.2 1.0
OD1 D:ASP98 4.7 77.5 1.0
C D:TYR115 4.7 78.3 1.0
O D:TYR115 4.8 77.2 1.0
HD12 B:LEU167 4.8 91.4 1.0
HD3 D:ARG102 4.8 81.8 1.0
HA B:ASP237 4.8 103.3 1.0
CB B:ASP237 4.9 86.4 1.0
HB3 D:ASP98 4.9 88.4 1.0
CA D:TYR115 4.9 74.3 1.0
HD13 B:LEU167 5.0 91.4 1.0
HD3 B:LYS240 5.0 135.8 1.0
HA D:ASP116 5.0 89.8 1.0

Calcium binding site 4 out of 7 in 9etj

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Calcium binding site 4 out of 7 in the Mouse Cnpase Catalytic Domain with Nanobody 10E


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Mouse Cnpase Catalytic Domain with Nanobody 10E within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca202

b:88.4
occ:1.00
O D:ASN97 2.5 82.5 1.0
OD2 D:ASP101 2.6 69.7 1.0
OD1 D:ASN97 3.4 71.0 1.0
O D:LEU99 3.4 71.7 1.0
HA D:ASP98 3.7 89.7 1.0
CG D:ASP101 3.7 69.0 1.0
C D:ASN97 3.8 73.1 1.0
HD2 D:PRO100 3.9 84.5 1.0
C D:LEU99 4.1 65.3 1.0
OD1 D:ASP101 4.1 70.8 1.0
H D:ASP101 4.2 82.4 1.0
O D:ASP31 4.3 74.3 1.0
CA D:ASP98 4.4 73.8 1.0
CG D:ASN97 4.5 71.7 1.0
N D:LEU99 4.5 76.2 1.0
H D:LEU99 4.5 92.6 1.0
N D:ASP98 4.5 71.1 1.0
C D:ASP98 4.5 71.3 1.0
HA D:ASN97 4.6 86.7 1.0
CD D:PRO100 4.6 69.5 1.0
N D:PRO100 4.6 86.2 1.0
CA D:ASN97 4.8 71.3 1.0
HB2 D:ASP101 4.9 81.8 1.0
HD3 D:PRO100 4.9 84.5 1.0
HG2 D:PRO53 4.9 96.3 1.0
CB D:ASP101 4.9 67.2 1.0
CA D:LEU99 5.0 69.8 1.0
N D:ASP101 5.0 67.8 1.0

Calcium binding site 5 out of 7 in 9etj

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Calcium binding site 5 out of 7 in the Mouse Cnpase Catalytic Domain with Nanobody 10E


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Mouse Cnpase Catalytic Domain with Nanobody 10E within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Ca201

b:76.9
occ:1.00
O F:ASN97 2.4 77.8 1.0
OD1 F:ASN97 2.6 77.6 1.0
OD1 F:ASP101 3.3 86.0 1.0
O F:ASP31 3.5 78.3 1.0
O F:LEU99 3.6 77.2 1.0
C F:ASN97 3.6 76.8 1.0
CG F:ASN97 3.8 80.7 1.0
HA F:ASN97 4.0 94.4 1.0
HA F:ASP98 4.2 91.0 1.0
CA F:ASN97 4.3 77.7 1.0
CG F:ASP101 4.4 85.1 1.0
C F:LEU99 4.6 74.4 1.0
HD2 F:PRO100 4.6 94.5 1.0
C F:ASP31 4.6 80.6 1.0
N F:ASP98 4.6 76.4 1.0
CB F:ASN97 4.6 79.9 1.0
HG3 F:PRO53 4.6 93.4 1.0
HG2 F:PRO53 4.7 93.4 1.0
HD22 F:ASN97 4.7 102.2 1.0
ND2 F:ASN97 4.7 84.2 1.0
OD2 F:ASP101 4.7 82.5 1.0
H F:LEU99 4.7 86.0 1.0
HA F:ASP31 4.7 100.0 1.0
CA F:ASP98 4.8 74.9 1.0
HB3 F:ASP31 4.8 98.3 1.0
N F:LEU99 4.8 70.7 1.0

Calcium binding site 6 out of 7 in 9etj

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Calcium binding site 6 out of 7 in the Mouse Cnpase Catalytic Domain with Nanobody 10E


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Mouse Cnpase Catalytic Domain with Nanobody 10E within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Ca201

b:156.4
occ:1.00
OD1 H:ASN97 2.3 89.8 1.0
O H:ASN97 2.7 84.6 1.0
O H:ASP31 3.1 83.5 1.0
CG H:ASN97 3.6 88.1 1.0
O H:LEU99 3.8 77.1 1.0
C H:ASN97 3.8 82.2 1.0
OD1 H:ASP101 3.9 71.5 1.0
HA H:ASN97 3.9 100.5 1.0
HB3 H:ASP31 4.2 103.2 1.0
HA H:ASP31 4.2 102.1 1.0
C H:ASP31 4.2 82.9 1.0
CA H:ASN97 4.3 82.8 1.0
HD21 H:ASN97 4.4 106.7 1.0
HA H:ASP98 4.4 92.8 1.0
ND2 H:ASN97 4.5 88.0 1.0
CB H:ASN97 4.5 85.8 1.0
CA H:ASP31 4.7 84.1 1.0
HG3 H:PRO53 4.7 97.7 1.0
C H:LEU99 4.8 75.4 1.0
HD2 H:PRO100 4.8 92.8 1.0
H H:LEU99 4.9 86.8 1.0
N H:ASP98 4.9 81.3 1.0
CB H:ASP31 4.9 85.1 1.0
HG2 H:PRO53 4.9 97.7 1.0
HA H:PHE32 5.0 97.7 1.0

Calcium binding site 7 out of 7 in 9etj

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Calcium binding site 7 out of 7 in the Mouse Cnpase Catalytic Domain with Nanobody 10E


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Mouse Cnpase Catalytic Domain with Nanobody 10E within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Ca202

b:95.5
occ:1.00
OD2 H:ASP98 2.4 83.2 1.0
OD1 H:ASP116 2.6 78.3 1.0
O H:PRO114 2.8 75.6 1.0
OD1 H:ASP96 2.8 79.3 1.0
CG H:ASP98 3.5 81.5 1.0
OD1 G:ASP237 3.5 78.8 1.0
CG H:ASP116 3.5 79.3 1.0
HB2 H:ASP98 3.5 95.2 1.0
OD2 H:ASP116 3.8 82.0 1.0
H H:ASP98 3.8 98.7 1.0
C H:PRO114 3.8 76.7 1.0
CG H:ASP96 3.8 77.8 1.0
HE2 G:TYR238 3.9 98.1 1.0
CB H:ASP98 4.0 78.4 1.0
HB3 H:PRO114 4.1 88.0 1.0
HA H:PRO114 4.3 89.8 1.0
OD2 H:ASP96 4.3 76.1 1.0
HA H:TYR115 4.4 95.6 1.0
OD1 H:ASP98 4.4 82.6 1.0
CA H:PRO114 4.4 73.9 1.0
HD2 G:TYR238 4.5 97.9 1.0
N H:ASP98 4.5 81.3 1.0
CG G:ASP237 4.5 79.8 1.0
HB2 H:PRO114 4.5 88.0 1.0
CB H:PRO114 4.6 72.4 1.0
H H:ASN97 4.7 98.2 1.0
C H:TYR115 4.7 80.5 1.0
CE2 G:TYR238 4.7 80.8 1.0
HA H:ASP96 4.7 95.6 1.0
HB3 H:ASP98 4.8 95.2 1.0
OD2 G:ASP237 4.8 79.2 1.0
O H:TYR115 4.8 81.7 1.0
N H:TYR115 4.8 77.0 1.0
HD3 H:ARG102 4.8 85.1 1.0
CA H:TYR115 4.9 78.8 1.0
HA H:ASP116 4.9 97.2 1.0
CB H:ASP116 4.9 79.9 1.0
N H:ASP116 4.9 81.5 1.0
CA H:ASP98 4.9 76.4 1.0

Reference:

S.Markusson, A.Raasakka, F.Opazo, P.Kursula. Mouse Cnpase Catalytic Domain with Nanobody 10E To Be Published.
Page generated: Sun Dec 15 09:47:24 2024

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