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Calcium in PDB 6sit: Pseudo-Atomic Crystal Structure of the Desmoglein 2 - Human Adenovirus Serotype 3 Fibre Knob Complex

Protein crystallography data

The structure of Pseudo-Atomic Crystal Structure of the Desmoglein 2 - Human Adenovirus Serotype 3 Fibre Knob Complex, PDB code: 6sit was solved by W.P.Burmeister, P.Fender, E.Vassal-Stermann, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 46.50 / 4.50
Space group I 21 3
Cell size a, b, c (Å), α, β, γ (°) 146.530, 146.530, 146.530, 90.00, 90.00, 90.00
R / Rfree (%) 36.7 / 37

Calcium Binding Sites:

The binding sites of Calcium atom in the Pseudo-Atomic Crystal Structure of the Desmoglein 2 - Human Adenovirus Serotype 3 Fibre Knob Complex (pdb code 6sit). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 6 binding sites of Calcium where determined in the Pseudo-Atomic Crystal Structure of the Desmoglein 2 - Human Adenovirus Serotype 3 Fibre Knob Complex, PDB code: 6sit:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in 6sit

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Calcium binding site 1 out of 6 in the Pseudo-Atomic Crystal Structure of the Desmoglein 2 - Human Adenovirus Serotype 3 Fibre Knob Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Pseudo-Atomic Crystal Structure of the Desmoglein 2 - Human Adenovirus Serotype 3 Fibre Knob Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca401

b:0.2
occ:1.00
 OD1 D:ASP136 2.0 0.2 1.0
OD2 D:ASP138 2.1 0.4 1.0
O D:ASN144 2.1 0.4 1.0
OD2 D:ASP136 2.5 0.9 1.0
CG D:ASP136 2.5 0.8 1.0
OD1 D:ASN104 2.5 0.8 1.0
OD2 D:ASP194 2.9 0.7 1.0
O D:ASN106 2.9 0.3 1.0
CG D:ASP138 3.0 0.4 1.0
OD1 D:ASP194 3.2 0.1 1.0
CB D:ASP138 3.3 0.5 1.0
C D:ASN144 3.3 0.8 1.0
CG D:ASP194 3.5 0.4 1.0
CG D:ASN104 3.7 0.6 1.0
OD1 D:ASN106 3.7 0.3 1.0
CB D:ASP136 4.0 0.8 1.0
OD1 D:ASP138 4.1 0.9 1.0
C D:ASN106 4.1 0.0 1.0
CA D:ASN144 4.1 0.3 1.0
N D:ASP138 4.3 0.2 1.0
N D:SER145 4.3 0.8 1.0
CB D:ASN144 4.3 0.1 1.0
CA D:ASP138 4.4 0.0 1.0
ND2 D:ASN104 4.4 0.6 1.0
CA D:SER145 4.5 0.0 1.0
CA D:ASN104 4.6 0.5 1.0
N D:ASN106 4.7 0.5 1.0
CB D:ASN104 4.8 0.6 1.0
CA D:ASP136 4.9 0.9 1.0
CG D:ASN106 4.9 0.6 1.0
C D:ASN104 4.9 0.2 1.0
CB D:ASP194 5.0 0.9 1.0
CA D:ASN106 5.0 0.2 1.0

Calcium binding site 2 out of 6 in 6sit

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Calcium binding site 2 out of 6 in the Pseudo-Atomic Crystal Structure of the Desmoglein 2 - Human Adenovirus Serotype 3 Fibre Knob Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Pseudo-Atomic Crystal Structure of the Desmoglein 2 - Human Adenovirus Serotype 3 Fibre Knob Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca402

b:0.2
occ:1.00
 OD1 D:ASP215 1.9 0.1 1.0
OE1 D:GLU121 2.3 0.8 1.0
OE2 D:GLU181 2.5 0.8 1.0
CG D:ASP215 2.9 0.7 1.0
O D:VAL216 3.0 0.3 1.0
OE1 D:GLU181 3.1 0.9 1.0
CD D:GLU181 3.1 0.7 1.0
N D:VAL216 3.1 0.6 1.0
CD D:GLU121 3.2 0.3 1.0
OD1 D:ASP218 3.4 0.5 1.0
OE2 D:GLU121 3.4 0.3 1.0
CA D:ASP215 3.6 0.9 1.0
NE D:ARG180 3.6 0.2 1.0
CB D:ARG180 3.7 0.4 1.0
OD1 D:ASP250 3.7 0.9 1.0
CB D:ASP215 3.7 0.5 1.0
OD2 D:ASP215 3.7 0.6 1.0
C D:ASP215 3.8 0.4 1.0
CD D:ARG180 4.0 0.2 1.0
C D:VAL216 4.0 0.2 1.0
CG2 D:VAL216 4.0 0.9 1.0
CA D:VAL216 4.1 0.4 1.0
CG D:ASP218 4.3 0.9 1.0
CA D:CA403 4.4 0.2 1.0
CG D:ARG180 4.5 0.2 1.0
CG D:GLU121 4.5 0.2 1.0
CG D:GLU181 4.6 0.7 1.0
CG D:ASP250 4.7 0.5 1.0
CB D:VAL216 4.7 0.6 1.0
CZ D:ARG180 4.7 0.5 1.0
CB D:GLU121 4.7 0.8 1.0
OD2 D:ASP218 4.8 0.2 1.0
CA D:ARG180 4.8 0.1 1.0
N D:GLU181 4.8 0.1 1.0
N D:ASP215 4.8 0.6 1.0
N D:ARG180 4.9 0.2 1.0
O D:LEU214 4.9 0.4 1.0
NH2 D:ARG180 5.0 0.8 1.0

Calcium binding site 3 out of 6 in 6sit

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Calcium binding site 3 out of 6 in the Pseudo-Atomic Crystal Structure of the Desmoglein 2 - Human Adenovirus Serotype 3 Fibre Knob Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Pseudo-Atomic Crystal Structure of the Desmoglein 2 - Human Adenovirus Serotype 3 Fibre Knob Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca403

b:0.2
occ:1.00
 OD2 D:ASP218 1.7 0.2 1.0
OE2 D:GLU121 2.0 0.3 1.0
CG D:ASP218 2.6 0.9 1.0
OE1 D:GLU181 2.7 0.9 1.0
OD1 D:ASP218 2.9 0.5 1.0
OD2 D:ASP179 2.9 0.0 1.0
CD D:GLU121 3.1 0.3 1.0
CG D:ASP179 3.3 0.3 1.0
OD1 D:ASP179 3.4 0.7 1.0
OE1 D:GLU121 3.7 0.8 1.0
CD D:GLU181 3.9 0.7 1.0
CB D:ASP218 4.1 0.9 1.0
OD1 D:ASN219 4.1 0.8 1.0
CG D:GLU121 4.2 0.2 1.0
CA D:CA402 4.4 0.2 1.0
CB D:ASP179 4.5 0.3 1.0
CA D:ASP179 4.7 0.9 1.0
OE2 D:GLU181 4.7 0.8 1.0
CG D:GLU181 4.8 0.7 1.0
N D:ARG180 4.8 0.2 1.0
CD2 D:LEU122 4.8 0.4 1.0
CB D:GLU181 4.8 0.9 1.0
O D:ASP218 4.9 0.2 1.0
CG D:LEU122 4.9 0.6 1.0
N D:GLU181 4.9 0.1 1.0
CD1 D:LEU122 5.0 0.7 1.0

Calcium binding site 4 out of 6 in 6sit

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Calcium binding site 4 out of 6 in the Pseudo-Atomic Crystal Structure of the Desmoglein 2 - Human Adenovirus Serotype 3 Fibre Knob Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Pseudo-Atomic Crystal Structure of the Desmoglein 2 - Human Adenovirus Serotype 3 Fibre Knob Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca404

b:0.2
occ:1.00
 O D:ASN256 2.1 0.5 1.0
ND2 D:ASN307 2.3 0.2 1.0
OD2 D:ASP248 2.3 0.1 1.0
OD1 D:ASN217 2.5 0.7 1.0
OD1 D:ASN307 2.6 0.4 1.0
OD1 D:ASP248 2.6 0.8 1.0
CG D:ASN307 2.7 0.6 1.0
O D:ASN219 2.7 0.6 1.0
OD2 D:ASP250 2.7 0.9 1.0
CG D:ASP248 2.8 0.7 1.0
C D:ASN256 3.3 0.1 1.0
CG D:ASN217 3.6 0.7 1.0
CG D:ASP250 3.8 0.5 1.0
C D:ASN219 3.9 0.5 1.0
CB D:ASN307 3.9 0.0 1.0
CB D:ASP250 4.1 0.9 1.0
N D:TRP257 4.1 0.4 1.0
CA D:TRP257 4.2 0.1 1.0
ND2 D:ASN217 4.2 0.7 1.0
CB D:ASP248 4.2 0.8 1.0
CA D:ASN256 4.2 0.0 1.0
CD D:PRO221 4.6 0.6 1.0
CB D:ASN217 4.7 1.0 1.0
CB D:ASN256 4.7 0.2 1.0
CG D:PRO221 4.7 0.5 1.0
CA D:ASN219 4.7 0.9 1.0
N D:ASN219 4.7 0.9 1.0
C D:TRP257 4.8 0.5 1.0
OD1 D:ASP250 4.9 0.9 1.0
CB D:ASN219 4.9 0.1 1.0
N D:ILE220 4.9 0.2 1.0
N D:PRO221 4.9 0.8 1.0
O D:TRP257 5.0 0.6 1.0

Calcium binding site 5 out of 6 in 6sit

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Calcium binding site 5 out of 6 in the Pseudo-Atomic Crystal Structure of the Desmoglein 2 - Human Adenovirus Serotype 3 Fibre Knob Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Pseudo-Atomic Crystal Structure of the Desmoglein 2 - Human Adenovirus Serotype 3 Fibre Knob Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca405

b:0.2
occ:1.00
 OD1 D:ASN332 2.3 0.1 1.0
O D:VAL333 2.5 1.0 1.0
OE2 D:GLU294 2.5 0.9 1.0
OE1 D:GLU335 2.5 0.4 1.0
OE1 D:GLU234 2.9 0.6 1.0
CG D:ASN332 3.3 0.1 1.0
CD D:GLU335 3.5 0.0 1.0
C D:VAL333 3.5 0.7 1.0
N D:VAL333 3.6 0.7 1.0
CD D:GLU294 3.7 0.2 1.0
ND2 D:ASN332 3.7 0.7 1.0
CG D:GLU335 3.9 0.5 1.0
CD D:GLU234 3.9 0.3 1.0
CA D:CA406 3.9 0.2 1.0
OE2 D:GLU234 4.1 0.1 1.0
CA D:VAL333 4.2 0.4 1.0
CB D:GLU335 4.4 0.7 1.0
N D:GLU335 4.5 0.1 1.0
OE2 D:GLU335 4.5 0.8 1.0
OE1 D:GLU294 4.5 0.7 1.0
N D:LYS334 4.5 0.9 1.0
CB D:ASN332 4.5 0.7 1.0
CG D:GLU294 4.6 0.5 1.0
C D:ASN332 4.6 0.5 1.0
CA D:ASN332 4.7 0.2 1.0
CA D:LYS334 4.8 0.2 1.0
C D:LYS334 4.9 0.5 1.0
CB D:VAL333 5.0 0.5 1.0

Calcium binding site 6 out of 6 in 6sit

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Calcium binding site 6 out of 6 in the Pseudo-Atomic Crystal Structure of the Desmoglein 2 - Human Adenovirus Serotype 3 Fibre Knob Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Pseudo-Atomic Crystal Structure of the Desmoglein 2 - Human Adenovirus Serotype 3 Fibre Knob Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca406

b:0.2
occ:1.00
 OE2 D:GLU234 2.1 0.1 1.0
OD1 D:ASP292 2.3 0.5 1.0
CG D:GLU294 2.5 0.5 1.0
OE1 D:GLU335 2.6 0.4 1.0
CD D:GLU234 2.9 0.3 1.0
OE2 D:GLU294 2.9 0.9 1.0
OE1 D:GLU234 3.2 0.6 1.0
CD D:GLU294 3.2 0.2 1.0
OE2 D:GLU335 3.2 0.8 1.0
CG D:ASP292 3.2 0.5 1.0
CD D:GLU335 3.3 0.0 1.0
OD2 D:ASP292 3.7 0.3 1.0
N D:GLU294 3.8 0.2 1.0
CB D:GLU294 3.8 0.1 1.0
N D:TYR293 3.9 1.0 1.0
CA D:CA405 3.9 0.2 1.0
CG D:GLU234 4.2 0.2 1.0
OE1 D:GLU294 4.4 0.7 1.0
CB D:ASP292 4.4 0.1 1.0
CA D:GLU294 4.4 0.9 1.0
C D:ASP292 4.5 0.2 1.0
CA D:ASP292 4.5 0.3 1.0
CA D:TYR293 4.6 0.9 1.0
CB D:TYR293 4.6 0.2 1.0
C D:TYR293 4.7 0.5 1.0
CG D:GLU335 4.8 0.5 1.0

Reference:

E.Vassal-Stermann, S.Hutin, P.Fender, W.P.Burmeister. Intermediate-Resolution Crystal Structure of the Human Adenovirus B Serotype 3 Fibre Knob in Complex with the EC2-EC3 Fragment of Desmoglein 2. Acta Crystallogr.,Sect.F V. 75 750 2019.
ISSN: ESSN 2053-230X
PubMed: 31797817
DOI: 10.1107/S2053230X19015784
Page generated: Tue Jul 16 14:48:05 2024

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