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Calcium in PDB 5e79: Macromolecular Diffractive Imaging Using Imperfect Crystals

Enzymatic activity of Macromolecular Diffractive Imaging Using Imperfect Crystals

All present enzymatic activity of Macromolecular Diffractive Imaging Using Imperfect Crystals:
1.10.3.9;

Protein crystallography data

The structure of Macromolecular Diffractive Imaging Using Imperfect Crystals, PDB code: 5e79 was solved by K.Ayyer, O.Yefanov, D.Oberthur, S.Roy-Chowdhury, L.Galli, V.Mariani, S.Basu, J.Coe, C.E.Conrad, R.Fromme, A.Schaffer, K.Dorner, D.James, C.Kupitz, M.Metz, G.Nelson, P.L.Xavier, K.R.Beyerlein, M.Schmidt, I.Sarrou, J.C.H.Spence, U.Weierstall, T.A.White, J.-H.Yang, Y.Zhao, M.Liang, A.Aquila, M.S.Hunter, J.E.Koglin, S.Boutet, P.Fromme, A.Barty, H.N.Chapman, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.98 / 3.50
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 250.800, 250.800, 250.800, 90.00, 90.00, 90.00
R / Rfree (%) 32.4 / 33.1

Other elements in 5e79:

The structure of Macromolecular Diffractive Imaging Using Imperfect Crystals also contains other interesting chemical elements:

Magnesium (Mg) 74 atoms
Manganese (Mn) 8 atoms
Iron (Fe) 6 atoms
Chlorine (Cl) 6 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Macromolecular Diffractive Imaging Using Imperfect Crystals (pdb code 5e79). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 8 binding sites of Calcium where determined in the Macromolecular Diffractive Imaging Using Imperfect Crystals, PDB code: 5e79:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Calcium binding site 1 out of 8 in 5e79

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Calcium binding site 1 out of 8 in the Macromolecular Diffractive Imaging Using Imperfect Crystals


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Macromolecular Diffractive Imaging Using Imperfect Crystals within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca601

b:65.3
occ:1.00
 CA1 A:OEX601 0.0 65.3 1.0
O1 A:OEX601 2.3 63.2 1.0
O2 A:OEX601 2.5 66.0 1.0
O5 A:OEX601 2.5 64.9 1.0
OD1 A:ASP170 2.9 64.6 1.0
O A:ALA344 2.9 66.4 1.0
OD2 A:ASP170 3.2 63.9 1.0
OE2 A:GLU189 3.3 65.9 1.0
CG A:ASP170 3.3 63.3 1.0
MN2 A:OEX601 3.4 63.6 1.0
OE1 A:GLU189 3.4 67.1 1.0
MN3 A:OEX601 3.4 64.2 1.0
MN1 A:OEX601 3.5 63.4 1.0
CD A:GLU189 3.7 65.3 1.0
MN4 A:OEX601 3.8 67.0 1.0
C A:ALA344 3.8 65.8 1.0
O3 A:OEX601 3.9 64.0 1.0
O4 A:OEX601 4.0 67.4 1.0
OXT A:ALA344 4.0 65.8 1.0
NH1 C:ARG357 4.1 67.2 1.0
OH A:TYR161 4.3 63.2 1.0
NH2 C:ARG357 4.5 64.7 1.0
CB A:ASP170 4.6 62.4 1.0
OE1 A:GLN165 4.8 64.6 1.0
CZ C:ARG357 4.8 68.2 1.0
CG A:GLN165 4.9 62.6 1.0
CB A:GLN165 5.0 63.0 1.0
OE1 A:GLU333 5.0 65.0 1.0

Calcium binding site 2 out of 8 in 5e79

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Calcium binding site 2 out of 8 in the Macromolecular Diffractive Imaging Using Imperfect Crystals


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Macromolecular Diffractive Imaging Using Imperfect Crystals within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca601

b:0.1
occ:1.00
 OE2 O:GLU181 3.6 86.9 1.0
OE2 B:GLU435 3.7 74.5 0.4
OD1 B:ASN438 3.7 69.9 1.0
OE1 O:GLU181 3.8 88.2 1.0
CD O:GLU181 4.1 85.8 1.0
O B:SER439 4.2 63.4 1.0
O B:THR434 4.4 65.9 1.0
CD B:GLU435 4.4 72.1 0.4
OE1 B:GLU435 4.7 73.2 0.4
CG B:ASN438 4.9 67.9 1.0
OG1 B:THR434 4.9 65.7 1.0

Calcium binding site 3 out of 8 in 5e79

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Calcium binding site 3 out of 8 in the Macromolecular Diffractive Imaging Using Imperfect Crystals


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Macromolecular Diffractive Imaging Using Imperfect Crystals within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Ca102

b:97.3
occ:1.00
 O F:ARG45 3.2 71.3 1.0
OE1 V:GLU23 3.6 86.4 1.0
OXT F:ARG45 3.7 71.5 1.0
C F:ARG45 4.0 71.8 1.0
OE2 V:GLU23 4.0 87.2 1.0
CD V:GLU23 4.1 84.8 1.0
O A:ALA309 4.5 69.2 1.0
CB A:ALA309 4.7 67.7 1.0

Calcium binding site 4 out of 8 in 5e79

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Calcium binding site 4 out of 8 in the Macromolecular Diffractive Imaging Using Imperfect Crystals


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Macromolecular Diffractive Imaging Using Imperfect Crystals within 5.0Å range:
probe atom residue distance (Å) B Occ
O:Ca301

b:90.0
occ:1.00
 OD1 O:ASN200 2.8 82.6 1.0
O O:THR138 2.8 84.4 1.0
O O:VAL201 3.4 80.2 1.0
CG O:ASN200 3.6 81.4 1.0
C O:THR138 3.8 84.4 1.0
ND2 O:ASN200 3.8 83.5 1.0
CA O:SER139 3.9 84.3 1.0
C O:SER139 4.2 84.0 1.0
N O:SER139 4.3 84.3 1.0
O O:SER139 4.4 84.0 1.0
O O:THR140 4.4 82.9 1.0
C O:VAL201 4.6 79.8 1.0
N O:VAL201 4.8 79.1 1.0
N O:THR140 4.9 83.8 1.0
CB O:ASN200 5.0 79.3 1.0

Calcium binding site 5 out of 8 in 5e79

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Calcium binding site 5 out of 8 in the Macromolecular Diffractive Imaging Using Imperfect Crystals


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Macromolecular Diffractive Imaging Using Imperfect Crystals within 5.0Å range:
probe atom residue distance (Å) B Occ
a:Ca601

b:86.0
occ:1.00
 CA1 a:OEX601 0.0 86.0 1.0
O1 a:OEX601 2.3 83.9 1.0
O2 a:OEX601 2.5 86.6 1.0
O5 a:OEX601 2.5 85.5 1.0
O a:ALA344 2.8 87.1 1.0
OD1 a:ASP170 3.0 85.3 1.0
OD2 a:ASP170 3.1 84.5 1.0
CG a:ASP170 3.3 84.0 1.0
MN2 a:OEX601 3.4 84.3 1.0
OE1 a:GLU189 3.4 87.8 1.0
MN3 a:OEX601 3.4 84.9 1.0
MN1 a:OEX601 3.5 84.0 1.0
MN4 a:OEX601 3.8 87.7 1.0
C a:ALA344 3.8 86.5 1.0
NH1 c:ARG357 3.9 87.8 1.0
OXT a:ALA344 3.9 86.4 1.0
O3 a:OEX601 3.9 84.7 1.0
O4 a:OEX601 4.0 88.0 1.0
OE2 a:GLU189 4.0 86.6 1.0
CD a:GLU189 4.1 86.0 1.0
NH2 c:ARG357 4.1 85.3 1.0
CZ c:ARG357 4.5 88.9 1.0
CB a:ASP170 4.7 83.1 1.0
OH a:TYR161 4.8 83.8 1.0
OE1 a:GLN165 4.9 85.3 1.0
CB a:GLN165 4.9 83.7 1.0
OE1 a:GLU333 5.0 85.6 1.0

Calcium binding site 6 out of 8 in 5e79

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Calcium binding site 6 out of 8 in the Macromolecular Diffractive Imaging Using Imperfect Crystals


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Macromolecular Diffractive Imaging Using Imperfect Crystals within 5.0Å range:
probe atom residue distance (Å) B Occ
b:Ca602

b:0.7
occ:1.00
 OD1 b:ASN438 3.5 90.5 1.0
OE2 b:GLU435 3.6 95.1 0.6
OE1 o:GLU181 3.8 0.9 1.0
OE2 o:GLU181 4.1 0.6 1.0
CD b:GLU435 4.4 92.8 0.6
CD o:GLU181 4.4 0.5 1.0
OE1 b:GLU435 4.5 93.8 0.6
O b:SER439 4.6 84.0 1.0
O b:THR434 4.6 86.5 1.0
CG b:ASN438 4.7 88.6 1.0
CA b:ASN438 5.0 85.9 1.0

Calcium binding site 7 out of 8 in 5e79

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Calcium binding site 7 out of 8 in the Macromolecular Diffractive Imaging Using Imperfect Crystals


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Macromolecular Diffractive Imaging Using Imperfect Crystals within 5.0Å range:
probe atom residue distance (Å) B Occ
f:Ca102

b:0.0
occ:1.00
 O f:ARG45 2.7 91.9 1.0
OXT f:ARG45 2.7 92.2 1.0
C f:ARG45 3.1 92.5 1.0
OE2 v:GLU23 3.3 0.9 1.0
OE1 v:GLU23 3.5 0.1 1.0
CD v:GLU23 3.7 0.4 1.0
CA f:ARG45 4.6 92.8 1.0
CG v:GLU23 5.0 0.6 1.0

Calcium binding site 8 out of 8 in 5e79

Go back to Calcium Binding Sites List in 5e79
Calcium binding site 8 out of 8 in the Macromolecular Diffractive Imaging Using Imperfect Crystals


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Macromolecular Diffractive Imaging Using Imperfect Crystals within 5.0Å range:
probe atom residue distance (Å) B Occ
o:Ca301

b:0.7
occ:1.00
 O o:THR138 2.4 0.0 1.0
OD1 o:ASN200 2.6 0.3 1.0
O o:VAL201 2.8 0.9 1.0
C o:THR138 3.5 0.1 1.0
CG o:ASN200 3.7 0.1 1.0
C o:VAL201 3.9 0.5 1.0
CA o:SER139 3.9 1.0 1.0
ND2 o:ASN200 4.1 0.1 1.0
N o:SER139 4.1 1.0 1.0
C o:SER139 4.3 0.7 1.0
O o:THR140 4.3 0.6 1.0
N o:VAL201 4.3 99.8 1.0
CA o:THR138 4.6 0.1 1.0
O o:SER139 4.6 0.6 1.0
CA o:VAL201 4.6 0.0 1.0
C o:ASN200 4.7 99.5 1.0
N o:THR140 4.8 0.4 1.0
N o:ALA202 4.9 0.0 1.0
CB o:ASN200 5.0 100.0 1.0

Reference:

K.Ayyer, O.M.Yefanov, D.Oberthur, S.Roy-Chowdhury, L.Galli, V.Mariani, S.Basu, J.Coe, C.E.Conrad, R.Fromme, A.Schaffer, K.Dorner, D.James, C.Kupitz, M.Metz, G.Nelson, P.L.Xavier, K.R.Beyerlein, M.Schmidt, I.Sarrou, J.C.Spence, U.Weierstall, T.A.White, J.H.Yang, Y.Zhao, M.Liang, A.Aquila, M.S.Hunter, J.S.Robinson, J.E.Koglin, S.Boutet, P.Fromme, A.Barty, H.N.Chapman. Macromolecular Diffractive Imaging Using Imperfect Crystals. Nature V. 530 202 2016.
ISSN: ESSN 1476-4687
PubMed: 26863980
DOI: 10.1038/NATURE16949
Page generated: Sun Jul 14 18:23:51 2024

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