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Calcium in PDB 9cmo: Cryo-Em Model Derived From Localized Reconstruction of AD657-Hexon-Fii Complex at 4.14A Resolution

Enzymatic activity of Cryo-Em Model Derived From Localized Reconstruction of AD657-Hexon-Fii Complex at 4.14A Resolution

All present enzymatic activity of Cryo-Em Model Derived From Localized Reconstruction of AD657-Hexon-Fii Complex at 4.14A Resolution:
3.4.21.5;

Calcium Binding Sites:

The binding sites of Calcium atom in the Cryo-Em Model Derived From Localized Reconstruction of AD657-Hexon-Fii Complex at 4.14A Resolution (pdb code 9cmo). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 7 binding sites of Calcium where determined in the Cryo-Em Model Derived From Localized Reconstruction of AD657-Hexon-Fii Complex at 4.14A Resolution, PDB code: 9cmo:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7;

Calcium binding site 1 out of 7 in 9cmo

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Calcium binding site 1 out of 7 in the Cryo-Em Model Derived From Localized Reconstruction of AD657-Hexon-Fii Complex at 4.14A Resolution


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Cryo-Em Model Derived From Localized Reconstruction of AD657-Hexon-Fii Complex at 4.14A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Ca1001

b:13.5
occ:1.00
 OG1 L:THR431 2.2 89.8 1.0
N L:THR431 2.3 89.8 1.0
CB L:THR431 2.9 89.8 1.0
CA L:THR431 3.1 89.8 1.0
C L:ASP430 3.3 86.6 1.0
CA L:ASP430 3.6 86.6 1.0
OE11 Z:CGU25 3.6 16.5 1.0
OE12 Z:CGU29 3.8 17.4 1.0
O L:THR431 4.0 89.8 1.0
C L:THR431 4.0 89.8 1.0
O L:THR429 4.3 86.6 1.0
CG2 L:THR431 4.3 89.8 1.0
CG1 K:VAL277 4.4 80.5 1.0
CB L:ASP430 4.4 86.6 1.0
O L:ASP430 4.4 86.6 1.0
CD1 Z:CGU25 4.6 16.1 1.0
N L:ASP430 4.7 86.6 1.0
CD2 Z:CGU29 4.7 12.2 1.0
CD1 Z:CGU29 4.8 16.8 1.0
OE22 Z:CGU29 4.9 10.3 1.0
OE21 Z:CGU29 4.9 14.5 1.0
CB K:VAL277 4.9 80.5 1.0
C L:THR429 4.9 86.6 1.0

Calcium binding site 2 out of 7 in 9cmo

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Calcium binding site 2 out of 7 in the Cryo-Em Model Derived From Localized Reconstruction of AD657-Hexon-Fii Complex at 4.14A Resolution


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Cryo-Em Model Derived From Localized Reconstruction of AD657-Hexon-Fii Complex at 4.14A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
Z:Ca601

b:14.3
occ:1.00
 OE12 Z:CGU7 2.4 13.2 1.0
OE21 Z:CGU29 2.8 14.5 1.0
CD1 Z:CGU7 3.6 13.1 1.0
O Z:CGU7 3.8 15.8 1.0
OE11 Z:CGU26 4.0 11.8 1.0
CD2 Z:CGU29 4.0 12.2 1.0
O L:THR429 4.0 86.6 1.0
CA Z:CA602 4.3 9.4 1.0
OE12 Z:CGU29 4.4 17.4 1.0
CG Z:CGU7 4.4 10.9 1.0
CB Z:CGU7 4.5 13.2 1.0
OE12 Z:CGU26 4.5 10.3 1.0
OE11 Z:CGU7 4.5 8.1 1.0
C Z:CGU7 4.5 17.0 1.0
CD1 Z:CGU29 4.6 16.8 1.0
CD2 Z:CGU7 4.6 9.3 1.0
CD1 Z:CGU26 4.7 14.3 1.0
OE22 Z:CGU29 4.7 10.3 1.0
CA Z:CGU7 4.8 13.4 1.0
OE22 Z:CGU7 4.9 8.1 1.0
CG Z:CGU29 5.0 13.0 1.0

Calcium binding site 3 out of 7 in 9cmo

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Calcium binding site 3 out of 7 in the Cryo-Em Model Derived From Localized Reconstruction of AD657-Hexon-Fii Complex at 4.14A Resolution


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Cryo-Em Model Derived From Localized Reconstruction of AD657-Hexon-Fii Complex at 4.14A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
Z:Ca602

b:9.4
occ:1.00
 OE12 Z:CGU26 2.4 10.3 1.0
OE21 Z:CGU16 2.5 4.8 1.0
OE11 Z:CGU7 2.5 8.1 1.0
OE22 Z:CGU16 2.9 9.0 1.0
OE12 Z:CGU7 3.0 13.2 1.0
CD2 Z:CGU16 3.1 8.4 1.0
CD1 Z:CGU7 3.1 13.1 1.0
CD1 Z:CGU26 3.5 14.3 1.0
OE21 Z:CGU29 3.6 14.5 1.0
OE12 Z:CGU6 3.8 15.9 1.0
OE11 Z:CGU26 4.1 11.8 1.0
O Z:ARG9 4.2 52.3 1.0
CA Z:CA603 4.3 12.6 1.0
CA Z:CA601 4.3 14.3 1.0
CD2 Z:CGU29 4.3 12.2 1.0
CA Z:CGU7 4.5 13.4 1.0
CG Z:CGU7 4.5 10.9 1.0
N Z:GLY11 4.6 61.8 1.0
CG Z:CGU16 4.6 7.4 1.0
CG Z:CGU26 4.6 13.6 1.0
CB Z:CGU29 4.6 11.0 1.0
CA Z:GLY11 4.8 61.8 1.0
O Z:CGU6 4.9 15.4 1.0
CD2 Z:CGU26 4.9 11.2 1.0
CG Z:CGU29 4.9 13.0 1.0
C Z:CGU7 4.9 17.0 1.0
CB Z:CGU26 4.9 14.9 1.0
OE11 Z:CGU29 4.9 20.6 1.0

Calcium binding site 4 out of 7 in 9cmo

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Calcium binding site 4 out of 7 in the Cryo-Em Model Derived From Localized Reconstruction of AD657-Hexon-Fii Complex at 4.14A Resolution


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Cryo-Em Model Derived From Localized Reconstruction of AD657-Hexon-Fii Complex at 4.14A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
Z:Ca603

b:12.6
occ:1.00
 OE12 Z:CGU6 2.4 15.9 1.0
OE22 Z:CGU26 2.4 10.6 1.0
OE12 Z:CGU16 2.4 12.4 1.0
OE11 Z:CGU7 2.4 8.1 1.0
N Z:ALA1 2.4 28.7 1.0
OE11 Z:CGU6 2.5 22.5 1.0
OE22 Z:CGU16 2.6 9.0 1.0
CD2 Z:CGU26 2.7 11.2 1.0
CD1 Z:CGU6 2.7 17.6 1.0
OE21 Z:CGU26 2.8 14.4 1.0
CD2 Z:CGU16 3.0 8.4 1.0
CD1 Z:CGU16 3.3 12.0 1.0
CD1 Z:CGU7 3.4 13.1 1.0
CA Z:ALA1 3.4 28.7 1.0
CA Z:CA604 3.6 12.1 1.0
CG Z:CGU16 3.6 7.4 1.0
CG Z:CGU7 3.7 10.9 1.0
OE21 Z:CGU16 3.7 4.8 1.0
O Z:ALA1 3.8 28.7 1.0
C Z:ALA1 3.9 28.7 1.0
CG Z:CGU26 3.9 13.6 1.0
CD1 Z:CGU26 4.1 14.3 1.0
OE12 Z:CGU26 4.1 10.3 1.0
CB Z:CGU16 4.2 11.1 1.0
CG Z:CGU6 4.2 18.2 1.0
CA Z:CA602 4.3 9.4 1.0
OE11 Z:CGU16 4.3 12.7 1.0
OE22 Z:CGU7 4.4 8.1 1.0
OE22 Z:CGU20 4.4 14.7 1.0
OE12 Z:CGU7 4.5 13.2 1.0
OE22 Z:CGU6 4.5 18.9 1.0
CD2 Z:CGU7 4.5 9.3 1.0
CB Z:CGU26 4.6 14.9 1.0
O Z:ASN2 4.7 40.0 1.0
OE11 Z:CGU26 4.7 11.8 1.0
CB Z:ALA1 4.8 28.7 1.0
CD2 Z:CGU6 4.8 19.5 1.0
CA Z:CGU7 4.8 13.4 1.0
CB Z:CGU7 4.8 13.2 1.0
CA Z:CGU16 4.9 12.2 1.0
N Z:ASN2 4.9 40.0 1.0
N Z:CGU7 5.0 13.0 1.0

Calcium binding site 5 out of 7 in 9cmo

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Calcium binding site 5 out of 7 in the Cryo-Em Model Derived From Localized Reconstruction of AD657-Hexon-Fii Complex at 4.14A Resolution


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Cryo-Em Model Derived From Localized Reconstruction of AD657-Hexon-Fii Complex at 4.14A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
Z:Ca604

b:12.1
occ:1.00
 N Z:ALA1 2.4 28.7 1.0
OE11 Z:CGU6 2.4 22.5 1.0
O Z:ASN2 2.4 40.0 1.0
OE22 Z:CGU20 2.5 14.7 1.0
OE22 Z:CGU6 2.6 18.9 1.0
N Z:ASN2 2.8 40.0 1.0
C Z:ALA1 2.8 28.7 1.0
OE12 Z:CGU16 2.8 12.4 1.0
CD2 Z:CGU20 3.0 10.2 1.0
CA Z:ALA1 3.0 28.7 1.0
OE21 Z:CGU20 3.3 12.8 1.0
C Z:ASN2 3.3 40.0 1.0
CD1 Z:CGU6 3.3 17.6 1.0
O Z:ALA1 3.5 28.7 1.0
CA Z:CA605 3.5 19.1 1.0
CA Z:CA603 3.6 12.6 1.0
CA Z:ASN2 3.6 40.0 1.0
CD2 Z:CGU6 3.6 19.5 1.0
OE12 Z:CGU20 3.6 19.0 1.0
CB Z:ALA1 3.6 28.7 1.0
OG1 Z:THR3 3.7 46.5 1.0
CD1 Z:CGU20 3.9 12.7 1.0
CD1 Z:CGU16 3.9 12.0 1.0
CG Z:CGU6 4.0 18.2 1.0
CG Z:CGU20 4.0 13.1 1.0
OE12 Z:CGU6 4.2 15.9 1.0
OE11 Z:CGU16 4.2 12.7 1.0
N Z:THR3 4.5 46.5 1.0
CB Z:CGU6 4.5 15.4 1.0
CB Z:ASN2 4.5 40.0 1.0
OE11 Z:CGU20 4.6 16.5 1.0
CB Z:CGU20 4.7 9.4 1.0
OE21 Z:CGU6 4.7 21.6 1.0
OE22 Z:CGU26 4.8 10.6 1.0
CB Z:THR3 4.9 46.5 1.0

Calcium binding site 6 out of 7 in 9cmo

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Calcium binding site 6 out of 7 in the Cryo-Em Model Derived From Localized Reconstruction of AD657-Hexon-Fii Complex at 4.14A Resolution


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Cryo-Em Model Derived From Localized Reconstruction of AD657-Hexon-Fii Complex at 4.14A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
Z:Ca605

b:19.1
occ:1.00
 OE21 Z:CGU20 2.4 12.8 1.0
OE11 Z:CGU20 2.5 16.5 1.0
CD1 Z:CGU20 2.8 12.7 1.0
CD2 Z:CGU20 2.9 10.2 1.0
CG Z:CGU20 3.3 13.1 1.0
OE22 Z:CGU6 3.3 18.9 1.0
OE12 Z:CGU20 3.5 19.0 1.0
CA Z:CA604 3.5 12.1 1.0
OG1 Z:THR3 3.7 46.5 1.0
OE22 Z:CGU20 3.8 14.7 1.0
CG2 Z:THR3 4.0 46.5 1.0
CD2 Z:CGU6 4.4 19.5 1.0
O Z:ASN2 4.4 40.0 1.0
CB Z:THR3 4.5 46.5 1.0
C Z:ASN2 4.7 40.0 1.0
CB Z:CGU20 4.7 9.4 1.0
OE21 Z:CGU6 4.8 21.6 1.0
N Z:ASN2 4.9 40.0 1.0

Calcium binding site 7 out of 7 in 9cmo

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Calcium binding site 7 out of 7 in the Cryo-Em Model Derived From Localized Reconstruction of AD657-Hexon-Fii Complex at 4.14A Resolution


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Cryo-Em Model Derived From Localized Reconstruction of AD657-Hexon-Fii Complex at 4.14A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
Z:Ca606

b:23.3
occ:1.00
 OE22 Z:CGU14 2.5 25.1 1.0
OE12 Z:CGU14 2.5 17.1 1.0
CD1 Z:CGU14 2.6 13.0 1.0
OE11 Z:CGU14 2.8 13.5 1.0
CD2 Z:CGU14 3.4 19.1 1.0
CG Z:CGU14 3.6 19.5 1.0
OE21 Z:CGU14 4.5 21.5 1.0
CB Z:CGU14 4.9 15.4 1.0
NH2 J:ARG456 5.0 88.0 1.0

Reference:

H.E.Mudrick, S.C.Lu, J.Bhandari, M.E.Barry, J.R.Hemsath, F.G.M.Andres, O.X.Ma, M.A.Barry, V.S.Reddy. Structure-Derived Insights From Blood Factors Binding to the Surfaces of Different Adenoviruses. Nat Commun V. 15 9768 2024.
ISSN: ESSN 2041-1723
PubMed: 39528527
DOI: 10.1038/S41467-024-54049-9
Page generated: Tue Dec 10 18:50:46 2024

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