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Calcium in PDB 5juh: Crystal Structure of C-Terminal Domain (Rv) of Mpafp

Protein crystallography data

The structure of Crystal Structure of C-Terminal Domain (Rv) of Mpafp, PDB code: 5juh was solved by S.Guo, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 39.42 / 1.35
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 34.960, 43.340, 78.840, 90.00, 90.00, 90.00
R / Rfree (%) 12.5 / 17.7

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of C-Terminal Domain (Rv) of Mpafp (pdb code 5juh). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 8 binding sites of Calcium where determined in the Crystal Structure of C-Terminal Domain (Rv) of Mpafp, PDB code: 5juh:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Calcium binding site 1 out of 8 in 5juh

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Calcium binding site 1 out of 8 in the Crystal Structure of C-Terminal Domain (Rv) of Mpafp


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of C-Terminal Domain (Rv) of Mpafp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca201

b:14.6
occ:1.00
 OD1 A:ASP129 2.2 18.9 1.0
O A:VAL133 2.3 15.6 1.0
O A:GLY135 2.3 17.3 1.0
OD1 A:ASN131 2.4 18.5 1.0
OD2 A:ASP140 2.4 15.7 1.0
OD1 A:ASP140 2.4 16.0 1.0
O A:HOH361 2.4 19.0 1.0
CG A:ASP140 2.7 14.9 1.0
CG A:ASP129 3.3 15.7 1.0
CG A:ASN131 3.4 17.6 1.0
C A:VAL133 3.4 19.9 1.0
C A:GLY135 3.5 16.3 1.0
ND2 A:ASN131 3.8 21.1 1.0
N A:VAL133 3.9 16.8 1.0
OD2 A:ASP129 4.1 22.2 1.0
CA A:ASP129 4.2 14.2 1.0
CB A:ASP129 4.2 14.6 1.0
CA A:VAL133 4.2 18.0 1.0
N A:GLY135 4.2 15.6 1.0
CB A:ASP140 4.3 13.2 1.0
CA A:GLY135 4.3 16.0 1.0
C A:ASP134 4.3 16.0 1.0
N A:ASN131 4.3 16.9 1.0
N A:GLY132 4.4 18.4 1.0
N A:VAL136 4.4 15.7 1.0
CA A:VAL136 4.4 14.6 1.0
N A:ASP134 4.5 17.8 1.0
N A:THR137 4.5 15.4 1.0
CB A:ASN131 4.6 18.0 1.0
C A:ASP129 4.6 15.2 1.0
N A:SER130 4.6 13.8 1.0
CA A:ASN131 4.7 18.9 1.0
CA A:ASP134 4.7 16.3 1.0
O A:ASP134 4.7 18.8 1.0
CB A:ASP134 4.8 20.5 1.0
C A:ASN131 4.8 19.5 1.0
CG2 A:VAL133 4.8 18.8 1.0
C A:GLY132 4.8 18.8 1.0
OG1 A:THR137 4.8 16.0 1.0
O A:HOH347 4.9 21.1 1.0
C A:VAL136 4.9 15.1 1.0

Calcium binding site 2 out of 8 in 5juh

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Calcium binding site 2 out of 8 in the Crystal Structure of C-Terminal Domain (Rv) of Mpafp


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of C-Terminal Domain (Rv) of Mpafp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca202

b:15.6
occ:0.50
 O A:HOH421 2.2 36.8 1.0
O A:HOH447 2.3 32.8 1.0
O A:THR56 2.3 17.0 1.0
OD1 A:ASP55 2.3 22.0 1.0
O A:HOH331 2.4 32.8 1.0
O A:HOH428 2.4 22.3 1.0
O A:HOH433 2.4 24.6 1.0
C A:THR56 3.4 16.2 1.0
CG A:ASP55 3.5 22.9 1.0
O A:HOH327 3.9 33.0 1.0
N A:THR56 3.9 14.6 1.0
O A:HOH379 4.0 43.4 1.0
OD2 A:ASP55 4.2 28.8 1.0
CA A:THR56 4.3 14.0 1.0
N A:THR57 4.3 13.6 1.0
CA A:THR57 4.4 13.9 1.0
C A:ASP55 4.5 16.3 1.0
CA A:ASP55 4.6 16.6 1.0
CB A:ASP55 4.6 22.3 1.0
OG1 A:THR56 4.7 17.7 1.0
O A:HOH332 4.9 34.9 1.0
C A:THR57 5.0 15.7 1.0

Calcium binding site 3 out of 8 in 5juh

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Calcium binding site 3 out of 8 in the Crystal Structure of C-Terminal Domain (Rv) of Mpafp


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of C-Terminal Domain (Rv) of Mpafp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca203

b:14.6
occ:1.00
 OD2 A:ASP36 2.2 16.6 1.0
O A:GLY33 2.3 16.3 1.0
O A:HOH424 2.3 20.1 1.0
O A:HOH439 2.4 20.2 1.0
O A:HOH416 2.4 25.6 1.0
OD2 A:ASP40 2.5 14.3 1.0
OD1 A:ASP40 2.5 19.6 1.0
CG A:ASP40 2.8 15.6 1.0
C A:GLY33 3.4 15.6 1.0
CG A:ASP36 3.4 14.8 1.0
CA A:CA204 4.0 12.7 1.0
CA A:GLY33 4.0 14.6 1.0
CB A:ASP36 4.1 16.9 1.0
CB A:ASP40 4.3 15.3 1.0
OD1 A:ASP36 4.4 16.1 1.0
O A:HOH340 4.5 14.8 1.0
N A:GLY34 4.5 14.5 1.0
O A:HOH392 4.6 26.7 1.0
O A:HOH389 4.7 28.5 1.0
O A:HOH417 4.7 48.7 1.0
O A:LEU38 4.8 14.8 1.0
CA A:GLY34 4.9 16.7 1.0

Calcium binding site 4 out of 8 in 5juh

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Calcium binding site 4 out of 8 in the Crystal Structure of C-Terminal Domain (Rv) of Mpafp


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystal Structure of C-Terminal Domain (Rv) of Mpafp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca204

b:12.7
occ:1.00
 O A:LEU38 2.3 14.8 1.0
O A:HOH340 2.4 14.8 1.0
OD1 A:ASP63 2.4 15.4 1.0
OD2 A:ASP40 2.4 14.3 1.0
OD1 A:ASP36 2.4 16.1 1.0
O A:HOH349 2.5 15.2 1.0
OD2 A:ASP36 2.6 16.6 1.0
CG A:ASP36 2.8 14.8 1.0
CG A:ASP63 3.3 14.3 1.0
CG A:ASP40 3.5 15.6 1.0
C A:LEU38 3.5 13.8 1.0
OD2 A:ASP63 3.5 17.1 1.0
N A:ASP40 3.8 14.4 1.0
CA A:CA203 4.0 14.6 1.0
CB A:ASP40 4.1 15.3 1.0
O A:GLY33 4.2 16.3 1.0
N A:LEU38 4.3 14.9 1.0
C A:VAL39 4.3 13.8 1.0
ND2 A:ASN54 4.3 15.9 1.0
CB A:ASP36 4.4 16.9 1.0
O A:GLY34 4.4 16.4 1.0
CA A:VAL39 4.4 13.8 1.0
N A:VAL39 4.4 13.7 1.0
O A:ASN61 4.4 13.8 1.0
OD1 A:ASN54 4.4 27.7 1.0
CA A:LEU38 4.4 14.9 1.0
OD1 A:ASP40 4.5 19.6 1.0
C A:GLY33 4.6 15.6 1.0
CA A:ASP40 4.6 13.4 1.0
O A:HOH364 4.7 21.7 1.0
CA A:GLY33 4.7 14.6 1.0
CB A:ASP63 4.8 12.7 1.0
CG A:ASN54 4.8 16.9 1.0
CB A:LEU38 5.0 16.2 1.0

Calcium binding site 5 out of 8 in 5juh

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Calcium binding site 5 out of 8 in the Crystal Structure of C-Terminal Domain (Rv) of Mpafp


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Crystal Structure of C-Terminal Domain (Rv) of Mpafp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca205

b:18.7
occ:1.00
 O A:LYS90 2.3 16.9 1.0
O A:HOH440 2.3 26.6 1.0
O A:HOH442 2.4 16.1 1.0
O A:HOH382 2.4 19.4 1.0
O A:HOH471 2.5 22.7 1.0
C A:LYS90 3.5 16.3 1.0
CA A:LYS90 4.3 17.9 1.0
CB A:LYS90 4.4 22.2 1.0
N A:ASP91 4.5 13.5 1.0
O A:HOH449 4.5 49.6 1.0
CA A:ASP91 4.6 15.0 1.0
OD1 A:ASP91 4.6 21.6 1.0
O A:HOH479 4.6 43.0 1.0

Calcium binding site 6 out of 8 in 5juh

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Calcium binding site 6 out of 8 in the Crystal Structure of C-Terminal Domain (Rv) of Mpafp


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Crystal Structure of C-Terminal Domain (Rv) of Mpafp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca206

b:13.0
occ:1.00
 OD2 A:ASP49 2.3 12.7 1.0
O A:LEU45 2.3 14.2 1.0
O A:GLY47 2.4 12.5 1.0
OD1 A:ASP73 2.4 12.0 1.0
O A:HOH436 2.4 11.3 0.5
O A:HOH330 2.4 15.4 1.0
CG A:ASP73 3.3 11.7 1.0
OD2 A:ASP73 3.4 12.2 1.0
CG A:ASP49 3.4 13.6 1.0
C A:GLY47 3.5 11.6 1.0
C A:LEU45 3.5 14.1 1.0
O A:GLU46 3.8 13.9 1.0
C A:GLU46 3.8 13.7 1.0
CB A:ASP49 4.0 11.3 1.0
N A:ASP49 4.1 10.7 1.0
C A:GLY44 4.1 12.3 1.0
N A:GLY47 4.1 13.2 1.0
O A:HOH436 4.2 15.7 0.5
CA A:GLU46 4.3 14.8 1.0
N A:LEU45 4.3 14.4 1.0
O A:GLY44 4.3 12.8 1.0
OD1 A:ASP49 4.3 12.3 1.0
O A:HOH372 4.3 26.1 1.0
CA A:GLY47 4.4 14.6 1.0
N A:GLU46 4.4 14.5 1.0
CA A:GLY44 4.4 13.3 1.0
N A:SER48 4.4 12.6 1.0
CA A:CA207 4.5 12.9 1.0
CA A:SER48 4.5 11.2 1.0
CA A:LEU45 4.6 14.2 1.0
CB A:ASP73 4.7 11.6 1.0
C A:SER48 4.7 14.0 1.0
CA A:ASP49 4.7 11.8 1.0
OD2 A:ASP67 4.7 17.1 1.0

Calcium binding site 7 out of 8 in 5juh

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Calcium binding site 7 out of 8 in the Crystal Structure of C-Terminal Domain (Rv) of Mpafp


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Crystal Structure of C-Terminal Domain (Rv) of Mpafp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca207

b:12.9
occ:1.00
 O A:GLU46 2.3 13.9 1.0
O A:GLY25 2.3 14.6 1.0
O A:GLY44 2.3 12.8 1.0
O A:GLY27 2.3 15.2 1.0
OD1 A:ASP49 2.4 12.3 1.0
OD2 A:ASP29 2.4 13.6 1.0
OD2 A:ASP49 2.8 12.7 1.0
CG A:ASP49 2.9 13.6 1.0
CG A:ASP29 3.4 16.7 1.0
C A:GLU46 3.5 13.7 1.0
C A:GLY44 3.5 12.3 1.0
C A:GLY25 3.5 14.8 1.0
C A:GLY27 3.6 13.9 1.0
N A:GLY25 3.9 13.7 1.0
C A:LEU45 3.9 14.1 1.0
O A:LEU45 4.0 14.2 1.0
N A:GLY27 4.1 15.7 1.0
C A:GLN26 4.2 17.1 1.0
N A:GLU46 4.2 14.5 1.0
CB A:ASP29 4.2 12.4 1.0
OD1 A:ASP29 4.2 18.1 1.0
N A:ASP29 4.3 12.1 1.0
CA A:GLY25 4.3 14.8 1.0
CA A:GLY44 4.3 13.3 1.0
CA A:GLY47 4.3 14.6 1.0
N A:GLY47 4.3 13.2 1.0
CB A:ASP49 4.4 11.3 1.0
N A:LEU45 4.4 14.4 1.0
N A:GLN26 4.4 16.1 1.0
CA A:GLY27 4.4 15.8 1.0
CA A:GLU46 4.4 14.8 1.0
CA A:LEU45 4.5 14.2 1.0
C A:GLY47 4.5 11.6 1.0
CA A:CA206 4.5 13.0 1.0
CA A:GLN26 4.5 18.3 1.0
O A:HOH334 4.5 14.7 1.0
O A:GLY47 4.5 12.5 1.0
N A:ASP28 4.6 13.4 1.0
O A:GLN26 4.6 22.2 1.0
CB A:LEU45 4.6 16.8 1.0
C A:GLY24 4.6 15.9 1.0
CA A:ASP28 4.7 11.9 1.0
CA A:GLY24 4.7 15.8 1.0
CA A:ASP29 4.9 12.0 1.0
C A:ASP28 5.0 15.5 1.0

Calcium binding site 8 out of 8 in 5juh

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Calcium binding site 8 out of 8 in the Crystal Structure of C-Terminal Domain (Rv) of Mpafp


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Crystal Structure of C-Terminal Domain (Rv) of Mpafp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca208

b:16.5
occ:0.80
 OE1 A:GLU46 2.3 24.4 1.0
O A:HOH429 2.4 25.8 1.0
OE2 A:GLU72 2.4 21.5 1.0
O A:HOH436 2.5 15.7 0.5
OE2 A:GLU46 2.5 24.4 1.0
OE1 A:GLU72 2.6 19.2 1.0
CD A:GLU72 2.8 18.7 1.0
CD A:GLU46 2.8 26.4 1.0
O A:HOH346 4.2 33.9 1.0
ND2 A:ASN69 4.2 19.8 1.0
CG A:GLU72 4.2 13.2 1.0
O A:HOH436 4.3 11.3 0.5
O A:HOH400 4.3 37.3 1.0
O A:HOH450 4.4 50.6 1.0
CG A:GLU46 4.4 20.1 1.0
O A:HOH477 4.5 21.7 1.0
O A:HOH306 4.7 42.8 1.0
N A:GLY47 4.8 13.2 1.0

Reference:

S.Guo, C.A.Stevens, T.D.R.Vance, L.L.C.Olijve, L.A.Graham, R.L.Campbell, S.R.Yazdi, C.Escobedo, M.Bar-Dolev, V.Yashunsky, I.Braslavsky, D.N.Langelaan, S.P.Smith, J.S.Allingham, I.K.Voets, P.L.Davies. Structure of A 1.5-Mda Adhesin That Binds Its Antarctic Bacterium to Diatoms and Ice. Sci Adv V. 3 01440 2017.
ISSN: ESSN 2375-2548
PubMed: 28808685
DOI: 10.1126/SCIADV.1701440
Page generated: Sat Dec 12 05:32:25 2020

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