Calcium in PDB 5swi: Crystal Structure of SPGH92 in Complex with Mannose

Protein crystallography data

The structure of Crystal Structure of SPGH92 in Complex with Mannose, PDB code: 5swi was solved by S.Shapiro-Ward, A.B.Boraston, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 127.76 / 2.15
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 130.003, 161.711, 208.404, 90.00, 90.00, 90.00
R / Rfree (%) 19.7 / 22.1

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of SPGH92 in Complex with Mannose (pdb code 5swi). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Crystal Structure of SPGH92 in Complex with Mannose, PDB code: 5swi:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 5swi

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Calcium binding site 1 out of 4 in the Crystal Structure of SPGH92 in Complex with Mannose


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 SPGH92 in Complex with Mannose within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca701

b:23.7
occ:1.00
O B:HOH1048 2.3 26.5 1.0
O B:HOH838 2.3 21.7 1.0
OD1 B:ASN557 2.4 24.8 1.0
OD2 B:ASP600 2.4 26.4 1.0
O3 B:GOL702 2.5 42.1 1.0
OE1 B:GLN558 2.5 22.6 1.0
O B:HOH892 2.6 23.4 1.0
O2 B:GOL702 2.6 37.0 1.0
C3 B:GOL702 3.4 44.0 1.0
CD B:GLN558 3.5 24.5 1.0
CG B:ASP600 3.5 25.6 1.0
CG B:ASN557 3.5 26.4 1.0
C2 B:GOL702 3.6 40.5 1.0
NE2 B:GLN558 3.8 26.4 1.0
OD1 B:ASP600 3.9 25.0 1.0
CB B:ASP598 4.2 24.6 1.0
OD1 B:ASP308 4.4 28.6 1.0
ND2 B:ASN557 4.4 28.6 1.0
N B:GLN558 4.5 24.6 1.0
CA B:ASN557 4.5 26.0 1.0
CB B:ASN557 4.5 26.7 1.0
C1 B:GOL702 4.6 44.0 1.0
OE2 B:GLU541 4.6 34.0 1.0
O B:HOH960 4.6 49.6 1.0
O B:HOH871 4.7 28.6 1.0
O B:SER556 4.8 25.4 1.0
CB B:ASP600 4.8 24.9 1.0
OD2 B:ASP598 4.8 26.9 1.0
CZ3 B:TRP307 4.8 35.2 1.0
O B:ASP598 4.8 22.5 1.0
CG B:GLN558 4.8 22.6 1.0
CG B:ASP598 5.0 27.0 1.0

Calcium binding site 2 out of 4 in 5swi

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Calcium binding site 2 out of 4 in the Crystal Structure of SPGH92 in Complex with Mannose


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 SPGH92 in Complex with Mannose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca709

b:17.6
occ:1.00
OD1 A:ASN557 2.3 15.4 1.0
OD2 A:ASP600 2.4 20.0 1.0
O3 A:GOL701 2.4 35.2 1.0
O2 A:GOL701 2.4 29.7 1.0
O A:HOH939 2.4 19.1 1.0
OE1 A:GLN558 2.4 17.9 1.0
O A:HOH971 2.5 17.5 1.0
O A:HOH834 2.6 19.7 1.0
C3 A:GOL701 3.3 38.6 1.0
C2 A:GOL701 3.4 34.3 1.0
CD A:GLN558 3.4 18.6 1.0
CG A:ASP600 3.5 21.0 1.0
CG A:ASN557 3.5 17.0 1.0
NE2 A:GLN558 3.8 20.5 1.0
OD1 A:ASP600 4.0 20.5 1.0
CB A:ASP598 4.2 20.2 1.0
OD1 A:ASP308 4.4 23.2 1.0
ND2 A:ASN557 4.4 16.9 1.0
CA A:ASN557 4.5 17.8 1.0
N A:GLN558 4.5 19.1 1.0
CB A:ASN557 4.5 16.9 1.0
C1 A:GOL701 4.5 34.3 1.0
OE2 A:GLU541 4.7 23.1 1.0
O A:SER556 4.7 20.2 1.0
CB A:ASP600 4.7 20.5 1.0
O A:ASP598 4.7 20.8 1.0
O A:HOH827 4.8 19.7 1.0
OD2 A:ASP598 4.8 23.4 1.0
CG A:GLN558 4.8 18.5 1.0
CZ3 A:TRP307 4.8 27.9 1.0
CG A:ASP598 4.9 20.0 1.0

Calcium binding site 3 out of 4 in 5swi

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Calcium binding site 3 out of 4 in the Crystal Structure of SPGH92 in Complex with Mannose


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 SPGH92 in Complex with Mannose within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca704

b:24.0
occ:1.00
O C:HOH846 2.2 28.6 1.0
OD2 C:ASP600 2.4 28.5 1.0
OD1 C:ASN557 2.4 29.1 1.0
O C:HOH1002 2.5 27.5 1.0
OE1 C:GLN558 2.5 25.2 1.0
O C:HOH914 2.5 27.1 1.0
O C:HOH809 2.6 27.1 1.0
O2 C:GOL701 2.9 35.5 1.0
CG C:ASP600 3.5 29.9 1.0
CD C:GLN558 3.5 25.5 1.0
CG C:ASN557 3.6 27.1 1.0
C2 C:GOL701 3.7 46.9 1.0
NE2 C:GLN558 3.8 27.1 1.0
OD1 C:ASP600 3.9 29.1 1.0
O3 C:GOL701 4.1 53.2 1.0
CB C:ASP598 4.2 26.5 1.0
C3 C:GOL701 4.2 50.4 1.0
OD1 C:ASP308 4.3 36.3 1.0
ND2 C:ASN557 4.4 28.1 1.0
CA C:ASN557 4.5 28.7 1.0
N C:GLN558 4.5 26.8 1.0
CB C:ASN557 4.6 27.6 1.0
OE2 C:GLU541 4.6 29.5 1.0
O C:HOH844 4.6 39.5 1.0
CB C:ASP600 4.7 28.6 1.0
O C:SER556 4.8 26.1 1.0
OD2 C:ASP598 4.8 31.3 1.0
O C:ASP598 4.8 24.4 1.0
CZ3 C:TRP307 4.8 43.7 1.0
O C:HOH838 4.8 23.8 1.0
CG C:GLN558 4.9 25.9 1.0
CG C:ASP598 4.9 27.7 1.0

Calcium binding site 4 out of 4 in 5swi

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Calcium binding site 4 out of 4 in the Crystal Structure of SPGH92 in Complex with Mannose


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 SPGH92 in Complex with Mannose within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca705

b:27.8
occ:1.00
OD1 D:ASN557 2.3 29.8 1.0
OD2 D:ASP600 2.4 29.5 1.0
O1 D:GOL701 2.4 40.7 1.0
O D:HOH888 2.5 28.9 1.0
OE1 D:GLN558 2.5 28.9 1.0
O D:HOH818 2.6 28.7 1.0
O D:HOH881 2.6 23.1 1.0
O2 D:GOL701 2.8 36.8 1.0
C1 D:GOL701 3.4 45.2 1.0
CG D:ASP600 3.5 31.8 1.0
CD D:GLN558 3.5 27.8 1.0
CG D:ASN557 3.5 28.7 1.0
C2 D:GOL701 3.6 42.5 1.0
NE2 D:GLN558 3.8 28.6 1.0
OD1 D:ASP600 3.9 32.7 1.0
CB D:ASP598 4.2 30.4 1.0
ND2 D:ASN557 4.4 28.5 1.0
OD1 D:ASP308 4.4 36.5 1.0
CA D:ASN557 4.4 30.2 1.0
N D:GLN558 4.5 29.5 1.0
CB D:ASN557 4.5 29.1 1.0
C3 D:GOL701 4.6 43.3 1.0
OE2 D:GLU541 4.6 30.0 1.0
O D:SER556 4.7 28.2 1.0
O D:HOH820 4.7 24.0 1.0
CB D:ASP600 4.7 31.1 1.0
O D:ASP598 4.7 27.1 1.0
OD2 D:ASP598 4.7 32.3 1.0
CG D:GLN558 4.9 27.8 1.0
CG D:ASP598 4.9 32.6 1.0
CZ3 D:TRP307 4.9 36.8 1.0

Reference:

M.Robb, J.K.Hobbs, S.A.Woodiga, S.Shapiro-Ward, M.D.Suits, N.Mcgregor, H.Brumer, H.Yesilkaya, S.J.King, A.B.Boraston. Molecular Characterization of N-Glycan Degradation and Transport in Streptococcus Pneumoniae and Its Contribution to Virulence. Plos Pathog. V. 13 06090 2017.
ISSN: ESSN 1553-7374
PubMed: 28056108
DOI: 10.1371/JOURNAL.PPAT.1006090
Page generated: Sat Dec 12 05:42:56 2020

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