Atomistry » Calcium » PDB 5ck1-5cxf » 5ckn
Atomistry »
  Calcium »
    PDB 5ck1-5cxf »
      5ckn »

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

Go back to Calcium Binding Sites List in 5ckn
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

Go back to Calcium Binding Sites List in 5ckn
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

Go back to Calcium Binding Sites List in 5ckn
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

Go back to Calcium Binding Sites List in 5ckn
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

Go back to Calcium Binding Sites List in 5ckn
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

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy