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Calcium in PDB 4wrf: Crystal Structure of Surfactant Protein-A Dedn Mutant (E171D/P175E/R197N/K203D) Complexed with Mannose

Protein crystallography data

The structure of Crystal Structure of Surfactant Protein-A Dedn Mutant (E171D/P175E/R197N/K203D) Complexed with Mannose, PDB code: 4wrf was solved by M.J.Rynkiewicz, H.Wu, T.R.Cafarella, N.M.Nikolaidis, J.F.Head, B.A.Seaton, F.X.Mccormack, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 14.93 / 1.90
Space group H 3 2
Cell size a, b, c (Å), α, β, γ (°) 69.157, 69.157, 169.566, 90.00, 90.00, 120.00
R / Rfree (%) 19.8 / 24.4

Other elements in 4wrf:

The structure of Crystal Structure of Surfactant Protein-A Dedn Mutant (E171D/P175E/R197N/K203D) Complexed with Mannose also contains other interesting chemical elements:

Chlorine (Cl) 1 atom

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Surfactant Protein-A Dedn Mutant (E171D/P175E/R197N/K203D) Complexed with Mannose (pdb code 4wrf). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the Crystal Structure of Surfactant Protein-A Dedn Mutant (E171D/P175E/R197N/K203D) Complexed with Mannose, PDB code: 4wrf:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in 4wrf

Go back to Calcium Binding Sites List in 4wrf
Calcium binding site 1 out of 3 in the Crystal Structure of Surfactant Protein-A Dedn Mutant (E171D/P175E/R197N/K203D) Complexed 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 Surfactant Protein-A Dedn Mutant (E171D/P175E/R197N/K203D) Complexed with Mannose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca401

b:32.0
occ:1.00
OD1 A:ASP215 2.3 35.7 1.0
OD1 A:ASN214 2.4 31.8 1.0
OE1 A:GLU202 2.4 40.5 1.0
OD1 A:ASN197 2.4 38.3 1.0
O A:ASP215 2.4 31.1 1.0
O3 A:MAN404 2.5 33.7 1.0
OE1 A:GLU195 2.5 39.1 1.0
O4 A:MAN404 2.7 33.3 1.0
CG A:ASP215 3.3 35.4 1.0
C3 A:MAN404 3.3 34.9 1.0
CG A:ASN214 3.4 29.6 1.0
C4 A:MAN404 3.4 34.0 1.0
CD A:GLU202 3.4 42.3 1.0
CD A:GLU195 3.5 39.5 1.0
CG A:ASN197 3.5 42.9 1.0
C A:ASP215 3.5 29.9 1.0
N A:ASP215 3.7 28.4 1.0
OE2 A:GLU195 3.8 39.9 1.0
OE2 A:GLU202 3.8 42.8 1.0
ND2 A:ASN214 3.8 29.9 1.0
OD2 A:ASP215 3.9 37.0 1.0
CA A:ASP215 4.0 29.8 1.0
ND2 A:ASN197 4.0 44.0 1.0
N A:ASN197 4.2 44.4 1.0
CB A:ASP215 4.2 32.0 1.0
N A:GLY198 4.5 53.2 1.0
C A:ASN214 4.5 27.6 1.0
N A:ARG216 4.6 27.3 1.0
CB A:ASN197 4.7 46.4 1.0
CB A:ASN214 4.7 27.6 1.0
C2 A:MAN404 4.7 36.1 1.0
CG A:GLU202 4.7 42.2 1.0
CG A:GLU195 4.7 38.2 1.0
CA A:ASN197 4.8 47.3 1.0
C A:ASN197 4.8 50.7 1.0
C5 A:MAN404 4.9 40.9 1.0
CA A:ASN214 4.9 27.3 1.0
CB A:GLU202 5.0 41.2 1.0
O2 A:MAN404 5.0 36.0 1.0

Calcium binding site 2 out of 3 in 4wrf

Go back to Calcium Binding Sites List in 4wrf
Calcium binding site 2 out of 3 in the Crystal Structure of Surfactant Protein-A Dedn Mutant (E171D/P175E/R197N/K203D) Complexed 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 Surfactant Protein-A Dedn Mutant (E171D/P175E/R197N/K203D) Complexed with Mannose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca402

b:34.9
occ:0.46
O A:HOH608 2.3 39.0 1.0
O A:HOH609 2.3 70.1 1.0
OD2 A:ASP171 2.4 53.9 1.0
OE1 A:GLU175 2.4 80.7 1.0
OE2 A:GLU175 2.4 80.2 1.0
OD1 A:ASP171 2.5 54.3 1.0
O A:GLU202 2.6 40.1 1.0
CD A:GLU175 2.8 82.6 1.0
CG A:ASP171 2.8 53.2 1.0
OD1 A:ASP203 3.1 45.9 1.0
C A:GLU202 3.2 40.6 1.0
N A:GLU202 3.8 51.1 1.0
N A:ASP203 3.9 37.8 1.0
N A:GLY200 3.9 80.8 1.0
CA A:ASP203 4.0 36.8 1.0
CA A:GLU202 4.1 43.6 1.0
C A:GLY200 4.2 83.3 1.0
CG A:ASP203 4.3 45.1 1.0
O A:GLY200 4.3 86.1 1.0
CG A:GLU175 4.3 88.7 1.0
CA A:GLY200 4.3 84.3 1.0
CB A:ASP171 4.3 50.9 1.0
CZ A:PHE178 4.5 36.8 1.0
N A:LYS201 4.6 75.8 1.0
CB A:GLU202 4.6 41.2 1.0
O A:ASP171 4.6 62.2 1.0
N A:GLN199 4.6 69.1 1.0
CB A:ASP203 4.7 39.8 1.0
N A:GLY176 4.8 81.8 1.0
OD2 A:ASP215 4.8 37.0 1.0
O A:HOH541 4.9 65.0 1.0
C A:GLY198 4.9 66.6 1.0
C A:LYS201 5.0 59.2 1.0
CA A:GLU175 5.0 92.7 1.0
C A:GLN199 5.0 78.2 1.0
CA A:CA403 5.0 58.6 0.6

Calcium binding site 3 out of 3 in 4wrf

Go back to Calcium Binding Sites List in 4wrf
Calcium binding site 3 out of 3 in the Crystal Structure of Surfactant Protein-A Dedn Mutant (E171D/P175E/R197N/K203D) Complexed 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 Surfactant Protein-A Dedn Mutant (E171D/P175E/R197N/K203D) Complexed with Mannose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca403

b:58.6
occ:0.62
OD2 A:ASP203 2.3 48.8 1.0
O A:GLY200 2.4 86.1 1.0
O A:HOH521 2.5 39.2 1.0
OD1 A:ASP203 2.5 45.9 1.0
CG A:ASP203 2.7 45.1 1.0
C A:GLY200 3.6 83.3 1.0
CB A:ASP203 4.2 39.8 1.0
OE1 A:GLU175 4.5 80.7 1.0
N A:LYS201 4.5 75.8 1.0
CA A:GLY200 4.5 84.3 1.0
CA A:LYS201 4.6 68.8 1.0
O A:ASP172 4.8 92.8 1.0
O A:HOH537 4.8 36.7 1.0
C A:LYS201 4.9 59.2 1.0
CA A:CA402 5.0 34.9 0.5

Reference:

M.J.Rynkiewicz, H.Wu, T.R.Cafarella, N.M.Nikolaidis, J.F.Head, B.A.Seaton, F.X.Mccormack. Differential Ligand Binding Specificities of the Pulmonary Collectins Are Determined By the Conformational Freedom of A Surface Loop To Be Published.
Page generated: Sat Dec 12 05:11:19 2020

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