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Calcium in PDB 5ckn: The CUB1-Egf-CUB2 Domains of Rat Mbl-Associated Serine Protease-2 (Masp-2) Bound to CA2+

Protein crystallography data

The structure of The CUB1-Egf-CUB2 Domains of Rat Mbl-Associated Serine Protease-2 (Masp-2) Bound to CA2+, PDB code: 5ckn was solved by R.Nan, C.M.Furze, D.W.Wright, J.Gor, R.Wallis, S.J.Perkins, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 63.55 / 2.60
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 83.640, 91.340, 127.090, 90.00, 90.00, 90.00
R / Rfree (%) 20.7 / 25.2

Calcium Binding Sites:

The binding sites of Calcium atom in the The CUB1-Egf-CUB2 Domains of Rat Mbl-Associated Serine Protease-2 (Masp-2) Bound to CA2+ (pdb code 5ckn). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 6 binding sites of Calcium where determined in the The CUB1-Egf-CUB2 Domains of Rat Mbl-Associated Serine Protease-2 (Masp-2) Bound to CA2+, PDB code: 5ckn:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in 5ckn

Go back to Calcium Binding Sites List in 5ckn
Calcium binding site 1 out of 6 in the The CUB1-Egf-CUB2 Domains of Rat Mbl-Associated Serine Protease-2 (Masp-2) Bound to CA2+


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of The CUB1-Egf-CUB2 Domains of Rat Mbl-Associated Serine Protease-2 (Masp-2) Bound to CA2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca300

b:59.2
occ:1.00
 OE2 A:GLU48 2.2 52.0 1.0
O A:HOH419 2.3 46.1 1.0
OD1 A:ASN104 2.3 50.4 1.0
OD1 A:ASP101 2.3 54.7 1.0
OD2 A:ASP56 2.4 56.4 1.0
O A:SER103 2.5 52.1 1.0
OD1 A:ASP56 2.5 52.6 1.0
CG A:ASP56 2.8 61.0 1.0
CG A:ASN104 3.3 62.0 1.0
CD A:GLU48 3.4 65.4 1.0
C A:SER103 3.4 54.0 1.0
CG A:ASP101 3.5 56.2 1.0
N A:ASP101 4.0 52.9 1.0
ND2 A:ASN104 4.1 60.7 1.0
OD2 A:ASP101 4.1 62.1 1.0
N A:ASN104 4.1 67.8 1.0
CB A:GLU48 4.1 51.8 1.0
OE1 A:GLU48 4.2 71.3 1.0
CA A:ASN104 4.2 68.0 1.0
CB A:ASP56 4.3 54.7 1.0
N A:SER103 4.4 69.1 1.0
CG A:GLU48 4.4 57.8 1.0
CB A:ASN104 4.4 65.8 1.0
CA A:SER103 4.5 60.2 1.0
O A:ASP101 4.5 56.1 1.0
CB A:ASP101 4.6 47.9 1.0
C A:ASP101 4.6 59.9 1.0
OD1 A:ASN22 4.6 69.5 1.0
CA A:ASP101 4.6 48.0 1.0
OH A:TYR20 4.7 44.4 1.0
CE1 A:TYR20 4.8 52.3 1.0
CB A:SER100 4.8 44.4 1.0
C A:SER100 4.9 58.7 1.0
CA A:SER100 5.0 47.6 1.0
N A:ASP56 5.0 51.6 1.0
CB A:TYR55 5.0 56.4 1.0

Calcium binding site 2 out of 6 in 5ckn

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Calcium binding site 2 out of 6 in the The CUB1-Egf-CUB2 Domains of Rat Mbl-Associated Serine Protease-2 (Masp-2) Bound to CA2+


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of The CUB1-Egf-CUB2 Domains of Rat Mbl-Associated Serine Protease-2 (Masp-2) Bound to CA2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca301

b:45.4
occ:1.00
 O A:VAL120 2.3 49.0 1.0
OD1 A:ASN139 2.3 61.8 1.0
O A:HOH408 2.5 56.7 1.0
OD1 A:ASP119 2.5 52.2 1.0
O A:TYR140 2.5 48.0 1.0
OE1 A:GLU122 2.6 59.1 1.0
O A:GLY143 2.6 63.5 1.0
OD2 A:ASP119 2.8 55.7 1.0
CG A:ASP119 3.0 50.6 1.0
CD A:GLU122 3.4 56.5 1.0
N A:GLY143 3.4 61.5 1.0
C A:GLY143 3.5 58.1 1.0
CG A:ASN139 3.5 61.2 1.0
OE2 A:GLU122 3.5 62.9 1.0
C A:VAL120 3.5 52.6 1.0
C A:TYR140 3.7 46.5 1.0
CA A:GLY143 3.8 54.5 1.0
N A:TYR140 4.0 45.0 1.0
N A:GLY142 4.0 56.7 1.0
ND2 A:ASN139 4.1 56.7 1.0
N A:VAL120 4.2 39.4 1.0
C A:GLY142 4.3 61.7 1.0
CA A:VAL120 4.4 45.4 1.0
O A:GLY35 4.4 57.8 1.0
CA A:TYR140 4.4 50.5 1.0
CB A:ASP119 4.5 44.8 1.0
N A:ASP121 4.5 49.0 1.0
CA A:ASP121 4.6 50.9 1.0
N A:LEU141 4.6 57.2 1.0
N A:GLU122 4.6 54.3 1.0
N A:TYR144 4.6 57.6 1.0
CA A:GLY142 4.7 51.2 1.0
C A:LEU141 4.7 52.1 1.0
CA A:LEU141 4.7 52.8 1.0
CB A:ASN139 4.7 52.6 1.0
C A:ASN139 4.8 50.5 1.0
C A:ASP119 4.8 43.7 1.0
CB A:VAL120 4.8 51.1 1.0
CG A:GLU122 4.8 52.4 1.0
CA A:ASN139 4.8 51.7 1.0

Calcium binding site 3 out of 6 in 5ckn

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Calcium binding site 3 out of 6 in the The CUB1-Egf-CUB2 Domains of Rat Mbl-Associated Serine Protease-2 (Masp-2) Bound to CA2+


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of The CUB1-Egf-CUB2 Domains of Rat Mbl-Associated Serine Protease-2 (Masp-2) Bound to CA2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca302

b:73.4
occ:1.00
 OD1 A:ASP262 2.3 78.7 1.0
OD2 A:ASP225 2.3 85.7 1.0
OE1 A:GLU215 2.4 0.1 1.0
O A:HOH420 2.4 76.4 1.0
O A:SER264 2.5 73.7 1.0
OD1 A:ASP225 2.6 75.5 1.0
O A:HOH417 2.7 73.8 1.0
CG A:ASP225 2.8 83.4 1.0
CG A:ASP262 3.4 74.4 1.0
CD A:GLU215 3.6 0.2 1.0
C A:SER264 3.7 68.5 1.0
CE1 A:TYR186 4.0 0.3 1.0
OH A:TYR186 4.0 0.3 1.0
OD2 A:ASP262 4.0 78.2 1.0
N A:ASP262 4.1 77.0 1.0
CB A:GLU215 4.1 0.6 1.0
NZ D:LYS65 4.3 0.6 1.0
CB A:ASP225 4.3 84.3 1.0
CA A:GLY265 4.3 85.7 1.0
N A:GLY265 4.4 73.0 1.0
OE2 A:GLU215 4.4 0.5 1.0
O A:ASP262 4.4 76.3 1.0
CZ A:TYR186 4.5 0.1 1.0
CG A:GLU215 4.5 0.9 1.0
N A:SER264 4.5 71.5 1.0
CB A:ASP262 4.6 69.1 1.0
C A:ASP262 4.6 78.7 1.0
CA A:ASP262 4.7 75.7 1.0
CA A:SER264 4.7 68.8 1.0
ND1 A:HIS267 4.8 0.3 1.0
CB A:THR261 4.9 69.0 1.0
CB A:TYR224 4.9 86.8 1.0

Calcium binding site 4 out of 6 in 5ckn

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Calcium binding site 4 out of 6 in the The CUB1-Egf-CUB2 Domains of Rat Mbl-Associated Serine Protease-2 (Masp-2) Bound to CA2+


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of The CUB1-Egf-CUB2 Domains of Rat Mbl-Associated Serine Protease-2 (Masp-2) Bound to CA2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca300

b:56.0
occ:1.00
 OD1 D:ASP101 2.3 70.6 1.0
OE2 D:GLU48 2.3 49.9 1.0
O D:HOH415 2.3 44.7 1.0
OD1 D:ASN104 2.4 68.4 1.0
O D:SER103 2.4 53.4 1.0
OD2 D:ASP56 2.4 64.2 1.0
OD1 D:ASP56 2.6 62.9 1.0
CG D:ASP56 2.8 61.4 1.0
CG D:ASN104 3.4 63.7 1.0
CG D:ASP101 3.5 58.5 1.0
C D:SER103 3.5 59.6 1.0
CD D:GLU48 3.6 49.2 1.0
N D:ASP101 4.0 61.9 1.0
ND2 D:ASN104 4.1 69.2 1.0
OD2 D:ASP101 4.1 55.0 1.0
NZ A:LYS65 4.1 73.8 1.0
CB D:GLU48 4.2 51.2 1.0
N D:ASN104 4.3 64.4 1.0
CB D:ASP56 4.3 53.5 1.0
N D:SER103 4.3 56.2 1.0
CA D:ASN104 4.3 59.2 1.0
OE1 D:GLU48 4.4 53.2 1.0
CB D:ASN104 4.5 50.8 1.0
O D:ASP101 4.5 67.3 1.0
CG D:GLU48 4.5 47.5 1.0
CA D:SER103 4.5 60.2 1.0
OD1 D:ASN22 4.5 66.6 1.0
C D:ASP101 4.5 58.9 1.0
CB D:ASP101 4.5 55.9 1.0
CA D:ASP101 4.6 57.5 1.0
OH D:TYR20 4.7 54.5 1.0
CE1 D:TYR20 4.8 58.9 1.0
CB D:SER100 4.8 47.9 1.0
CB D:TYR55 4.9 58.5 1.0
C D:SER100 4.9 59.0 1.0
N D:ASP56 5.0 48.2 1.0
CA D:SER100 5.0 51.4 1.0

Calcium binding site 5 out of 6 in 5ckn

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Calcium binding site 5 out of 6 in the The CUB1-Egf-CUB2 Domains of Rat Mbl-Associated Serine Protease-2 (Masp-2) Bound to CA2+


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of The CUB1-Egf-CUB2 Domains of Rat Mbl-Associated Serine Protease-2 (Masp-2) Bound to CA2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca301

b:55.6
occ:1.00
 OD1 D:ASN139 2.3 55.1 0.8
O D:HOH411 2.3 48.6 1.0
O D:VAL120 2.4 59.7 1.0
O D:TYR140 2.5 62.5 1.0
OE1 D:GLU122 2.6 66.6 1.0
OD1 D:ASP119 2.6 57.8 1.0
O D:GLY143 2.7 55.9 1.0
OD2 D:ASP119 2.9 53.0 1.0
CG D:ASP119 3.1 47.4 1.0
CG D:ASN139 3.3 56.7 0.8
N D:GLY143 3.3 53.1 1.0
C D:GLY143 3.5 52.6 1.0
CD D:GLU122 3.5 67.4 1.0
C D:VAL120 3.6 62.5 1.0
C D:TYR140 3.7 61.2 1.0
ND2 D:ASN139 3.7 53.2 0.8
OE2 D:GLU122 3.7 61.2 1.0
CA D:GLY143 3.8 53.7 1.0
N D:TYR140 3.9 62.8 1.0
N D:GLY142 4.0 65.4 1.0
C D:GLY142 4.2 68.6 1.0
N D:VAL120 4.4 63.8 1.0
CA D:ASP121 4.4 61.9 1.0
CB D:ASN139 4.5 55.1 0.2
N D:ASP121 4.5 63.6 1.0
CA D:TYR140 4.5 60.1 1.0
N D:GLU122 4.5 66.3 1.0
CA D:GLY142 4.5 54.0 1.0
CB D:ASN139 4.6 52.4 0.8
CB D:ASP119 4.6 43.1 1.0
CA D:VAL120 4.6 65.1 1.0
N D:TYR144 4.6 58.0 1.0
N D:LEU141 4.6 63.3 1.0
C D:LEU141 4.7 60.8 1.0
O D:GLY35 4.7 56.2 1.0
CA D:ASN139 4.7 54.2 0.2
CA D:ASN139 4.7 54.3 0.8
CA D:LEU141 4.7 56.2 1.0
C D:ASN139 4.8 55.0 1.0
C D:ASP119 4.9 45.2 1.0
CG D:GLU122 4.9 64.0 1.0

Calcium binding site 6 out of 6 in 5ckn

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Calcium binding site 6 out of 6 in the The CUB1-Egf-CUB2 Domains of Rat Mbl-Associated Serine Protease-2 (Masp-2) Bound to CA2+


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of The CUB1-Egf-CUB2 Domains of Rat Mbl-Associated Serine Protease-2 (Masp-2) Bound to CA2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca302

b:0.1
occ:1.00
 OD2 D:ASP225 2.4 0.9 1.0
O D:SER264 2.5 0.0 1.0
OD1 D:ASP262 2.6 0.3 1.0
OE1 D:GLU215 2.7 0.6 1.0
O D:HOH413 2.7 64.4 1.0
CG D:ASP225 3.2 0.6 1.0
OD1 D:ASP225 3.2 0.4 1.0
C D:SER264 3.5 1.0 1.0
CD D:GLU215 3.7 0.6 1.0
CG D:ASP262 3.7 0.8 1.0
CA D:GLY265 3.7 0.1 1.0
CE1 D:TYR186 3.8 95.0 1.0
OH D:TYR186 3.8 98.5 1.0
ND1 D:HIS267 4.0 0.0 1.0
N D:GLY265 4.1 0.8 1.0
OD2 D:ASP262 4.1 0.6 1.0
CB D:GLU215 4.2 0.0 1.0
CZ D:TYR186 4.2 0.2 1.0
CE1 D:HIS267 4.3 0.5 1.0
C D:GLY265 4.4 0.9 1.0
OE2 D:GLU215 4.4 0.3 1.0
CG D:GLU215 4.5 0.8 1.0
N D:ASP262 4.5 0.8 1.0
CB D:ASP225 4.6 0.1 1.0
O D:GLY265 4.7 0.2 1.0
CA D:SER264 4.8 0.6 1.0
N D:SER264 4.8 0.9 1.0
CD1 D:TYR186 4.9 88.7 1.0
O D:ASP262 4.9 0.8 1.0
CB D:ASP262 4.9 0.5 1.0
CG D:HIS267 4.9 0.4 1.0

Reference:

R.Nan, C.M.Furze, D.W.Wright, J.Gor, R.Wallis, S.J.Perkins. Flexibility in Mannan-Binding Lectin-Associated Serine Proteases-1 and -2 Provides Insight on Lectin Pathway Activation. Structure V. 25 364 2017.
ISSN: ISSN 1878-4186
PubMed: 28111019
DOI: 10.1016/J.STR.2016.12.014
Page generated: Sun Jul 14 17:11:32 2024

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