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Calcium in PDB 5hl3: Crystal Structure of Listeria Monocytogenes Inlp

Protein crystallography data

The structure of Crystal Structure of Listeria Monocytogenes Inlp, PDB code: 5hl3 was solved by S.Nocadello, S.H.Light, G.Minasov, O.Kiryukhina, K.Kwon, C.Faralla, A.Bakardjiev, W.F.Anderson, Center For Structural Genomics Ofinfectious Diseases (Csgid), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 1.40
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 72.883, 72.883, 179.449, 90.00, 90.00, 90.00
R / Rfree (%) 16 / 17.6

Other elements in 5hl3:

The structure of Crystal Structure of Listeria Monocytogenes Inlp also contains other interesting chemical elements:

Chlorine (Cl) 1 atom

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Listeria Monocytogenes Inlp (pdb code 5hl3). 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 Listeria Monocytogenes Inlp, PDB code: 5hl3:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Calcium binding site 1 out of 8 in 5hl3

Go back to Calcium Binding Sites List in 5hl3
Calcium binding site 1 out of 8 in the Crystal Structure of Listeria Monocytogenes Inlp


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 Listeria Monocytogenes Inlp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca401

b:11.4
occ:1.00
 O A:GLY135 2.2 13.0 1.0
OD1 A:ASP132 2.3 12.1 1.0
O A:PRO133 2.4 12.8 1.0
O A:HOH721 2.5 15.1 1.0
O A:HOH549 2.5 10.9 1.0
O A:HOH926 2.5 15.4 1.0
O A:HOH925 2.7 11.8 1.0
CG A:ASP132 3.4 12.0 1.0
C A:GLY135 3.4 13.3 1.0
C A:PRO133 3.6 12.8 1.0
OD2 A:ASP132 4.0 12.8 1.0
C A:PRO134 4.1 13.4 1.0
N A:PRO133 4.1 12.4 1.0
N A:GLY135 4.2 13.5 1.0
C A:ASP132 4.2 12.2 1.0
CA A:ARG136 4.3 13.2 0.5
O A:PRO134 4.3 13.4 1.0
O A:HOH891 4.3 30.7 1.0
N A:ARG136 4.3 13.4 0.5
N A:ARG136 4.3 13.4 0.5
CA A:ARG136 4.3 13.2 0.5
OE1 A:GLU182 4.3 13.9 1.0
O A:HOH647 4.4 18.5 1.0
CA A:PRO133 4.4 12.7 1.0
O A:GLY159 4.4 12.2 1.0
CA A:GLY135 4.4 13.6 1.0
CD A:PRO133 4.5 12.4 1.0
N A:LEU137 4.5 12.9 1.0
N A:PRO134 4.5 13.1 1.0
CA A:PRO134 4.5 13.4 1.0
O A:ASP132 4.5 12.3 1.0
O A:HOH1130 4.6 29.2 1.0
CB A:ASP132 4.6 11.9 1.0
O A:HOH780 4.6 21.3 1.0
CA A:ASP132 4.8 12.0 1.0
CA A:GLY159 4.8 11.8 1.0
C A:ARG136 4.9 13.2 0.5
C A:ARG136 4.9 13.2 0.5
O A:HOH653 4.9 10.7 1.0

Calcium binding site 2 out of 8 in 5hl3

Go back to Calcium Binding Sites List in 5hl3
Calcium binding site 2 out of 8 in the Crystal Structure of Listeria Monocytogenes Inlp


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 Listeria Monocytogenes Inlp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca402

b:18.2
occ:1.00
 OD1 A:ASP65 2.3 16.1 1.0
O A:HOH1002 2.3 35.2 1.0
O A:HOH924 2.4 19.6 1.0
O A:HOH1240 2.4 34.1 1.0
O A:HOH757 2.5 37.9 1.0
CG A:ASP65 3.4 14.8 1.0
OD2 A:ASP65 3.8 15.9 1.0
O A:HOH1058 4.5 37.3 1.0
O A:HOH987 4.7 19.2 1.0
CB A:ASP65 4.7 13.9 1.0
CB A:SER62 4.8 15.9 1.0
O A:HOH532 5.0 16.8 0.5

Calcium binding site 3 out of 8 in 5hl3

Go back to Calcium Binding Sites List in 5hl3
Calcium binding site 3 out of 8 in the Crystal Structure of Listeria Monocytogenes Inlp


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 Listeria Monocytogenes Inlp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca403

b:12.0
occ:1.00
 O A:HOH685 2.4 14.1 1.0
OE2 A:GLU108 2.5 14.1 1.0
O A:HOH747 2.5 13.0 1.0
OE1 A:GLU108 2.6 14.3 1.0
CD A:GLU108 2.9 14.1 1.0
CG A:GLU108 4.4 13.8 1.0
O A:HOH542 4.5 20.1 1.0
O A:GLU81 4.6 13.3 1.0
OE1 A:GLU81 4.6 14.7 1.0
O A:HOH619 4.8 22.1 1.0
O A:HOH1010 4.9 17.0 0.4
O A:HOH1010 4.9 17.2 0.6
CD A:GLU81 4.9 14.1 1.0

Calcium binding site 4 out of 8 in 5hl3

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Calcium binding site 4 out of 8 in the Crystal Structure of Listeria Monocytogenes Inlp


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 Listeria Monocytogenes Inlp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca404

b:12.3
occ:1.00
 O A:HOH1078 2.3 23.1 1.0
O A:HOH667 2.3 17.0 1.0
O A:HOH836 2.4 16.9 1.0
O A:LEU184 2.4 12.5 1.0
O A:HOH628 2.4 15.3 1.0
OE1 A:GLU189 2.5 12.6 1.0
OE2 A:GLU189 2.6 13.3 1.0
CD A:GLU189 2.8 12.8 1.0
C A:LEU184 3.6 12.3 1.0
O A:LEU162 4.2 12.8 1.0
CA A:ILE185 4.2 12.0 1.0
O A:HOH581 4.3 33.3 1.0
N A:ILE185 4.3 12.0 1.0
CG A:GLU189 4.4 12.8 1.0
OG1 A:THR186 4.4 13.0 1.0
N A:THR186 4.4 12.3 1.0
CB A:LEU184 4.5 12.7 1.0
O A:HOH990 4.5 37.1 1.0
O A:HOH597 4.5 22.2 1.0
O A:HOH966 4.5 36.4 1.0
O A:GLY164 4.6 13.3 1.0
CA A:LEU184 4.6 12.3 1.0
O A:MSE183 4.7 12.1 1.0
O A:HOH587 4.7 25.5 1.0
O A:HOH1276 4.7 39.5 1.0
C A:ILE185 4.8 12.1 1.0
OD1 A:ASN161 4.9 17.1 1.0

Calcium binding site 5 out of 8 in 5hl3

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Calcium binding site 5 out of 8 in the Crystal Structure of Listeria Monocytogenes Inlp


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 Listeria Monocytogenes Inlp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca405

b:10.9
occ:1.00
 OD1 A:ASN217 2.3 13.6 1.0
OD1 A:ASN194 2.4 13.9 1.0
OE1 A:GLN216 2.4 14.0 1.0
O A:HOH1012 2.4 12.1 1.0
O A:HOH771 2.4 13.4 1.0
O A:HOH818 2.5 15.0 1.0
CG A:ASN217 3.4 13.6 1.0
CG A:ASN194 3.5 13.8 1.0
CD A:GLN216 3.6 13.9 1.0
ND2 A:ASN217 3.8 13.9 1.0
CB A:GLN216 3.9 13.5 1.0
ND2 A:ASN194 4.3 13.7 1.0
CG A:GLN216 4.3 13.6 1.0
O A:HOH669 4.3 15.8 1.0
O A:HOH1056 4.5 18.0 1.0
O A:HOH1025 4.5 30.3 1.0
CB A:ASN194 4.6 13.6 1.0
O A:HOH1048 4.6 32.2 1.0
NE2 A:GLN216 4.6 14.1 1.0
CB A:ASN217 4.7 13.3 1.0
O A:ASN192 4.8 13.0 1.0
CA A:ASN194 4.8 13.3 1.0
O A:HOH1017 4.9 24.1 1.0

Calcium binding site 6 out of 8 in 5hl3

Go back to Calcium Binding Sites List in 5hl3
Calcium binding site 6 out of 8 in the Crystal Structure of Listeria Monocytogenes Inlp


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 Listeria Monocytogenes Inlp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca406

b:29.2
occ:1.00
 O A:HOH869 2.3 36.0 1.0
OD1 A:ASN349 2.3 22.0 1.0
O A:HOH948 2.3 35.4 1.0
O A:GLU346 2.4 27.4 0.5
O A:GLU346 2.4 27.2 0.5
OE1 A:GLU346 2.5 24.9 0.5
O A:HOH949 2.5 39.5 1.0
O A:HOH1133 2.7 43.5 1.0
CG A:ASN349 3.4 20.9 1.0
C A:GLU346 3.5 27.0 0.5
C A:GLU346 3.5 27.2 0.5
CD A:GLU346 3.7 24.5 0.5
ND2 A:ASN349 3.8 21.1 1.0
CA A:GLU346 4.1 25.6 0.5
CA A:GLU346 4.2 26.1 0.5
CB A:GLU346 4.3 25.9 0.5
O A:GLU347 4.4 30.5 1.0
OE2 A:GLU346 4.5 24.1 0.5
N A:GLU347 4.6 29.2 1.0
CD1 A:PHE315 4.6 16.0 1.0
CG A:GLU346 4.7 25.2 0.5
O A:HOH800 4.7 24.4 1.0
CB A:GLU346 4.7 27.1 0.5
CB A:ASN349 4.7 20.0 1.0
CA A:GLU347 4.8 31.3 1.0
C A:GLU347 4.8 29.6 1.0
N A:ASN349 4.8 21.8 1.0
CA A:ASN349 4.9 19.9 1.0

Calcium binding site 7 out of 8 in 5hl3

Go back to Calcium Binding Sites List in 5hl3
Calcium binding site 7 out of 8 in the Crystal Structure of Listeria Monocytogenes Inlp


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 Listeria Monocytogenes Inlp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca407

b:20.2
occ:1.00
 O A:HOH916 2.3 32.2 1.0
OD1 A:ASP382 2.3 20.7 1.0
OG A:SER380 2.4 13.7 1.0
O A:HOH692 2.4 29.2 1.0
O A:HOH1000 2.4 28.7 1.0
O A:HOH874 2.5 20.5 1.0
OD2 A:ASP366 2.5 16.8 1.0
CG A:ASP382 3.2 17.9 1.0
OD2 A:ASP382 3.3 22.0 1.0
CG A:ASP366 3.7 16.2 1.0
CB A:SER380 3.7 13.3 1.0
CB A:ASP366 4.3 15.7 1.0
C A:SER380 4.4 12.7 1.0
O A:HOH858 4.4 26.4 1.0
O A:HOH984 4.5 40.5 1.0
CB A:ASP382 4.6 16.0 1.0
N A:TYR381 4.6 12.8 1.0
O A:SER380 4.6 12.4 1.0
OD1 A:ASP366 4.6 17.0 1.0
CA A:SER380 4.7 12.9 1.0
O A:HOH540 4.7 24.1 1.0
O A:HOH1139 4.7 34.8 1.0
C A:TYR381 4.8 13.1 1.0
N A:ASP382 4.9 13.5 1.0
ND2 A:ASN293 4.9 13.1 1.0

Calcium binding site 8 out of 8 in 5hl3

Go back to Calcium Binding Sites List in 5hl3
Calcium binding site 8 out of 8 in the Crystal Structure of Listeria Monocytogenes Inlp


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 Listeria Monocytogenes Inlp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca408

b:19.6
occ:1.00
 OD1 A:ASN100 2.3 13.9 1.0
O A:HOH722 2.3 20.3 1.0
O A:HOH746 2.4 20.0 1.0
O A:HOH764 2.5 18.1 1.0
CG A:ASN100 3.5 13.5 1.0
O A:HOH810 4.1 22.1 1.0
O A:ASN99 4.2 13.5 1.0
O A:HOH1167 4.2 31.1 1.0
CB A:ASN100 4.4 13.2 1.0
ND2 A:ASN100 4.4 13.3 1.0
CA A:ASN100 4.5 13.1 1.0
O A:HOH680 4.6 15.7 1.0
O A:HOH1071 4.6 33.9 1.0
C A:ASN99 4.9 13.1 1.0

Reference:

S.Nocadello, S.H.Light, G.Minasov, O.Kiryukhina, K.Kwon, C.Faralla, A.Bakardjiev, W.F.Anderson. Crystal Structure of Listeria Monocytogenes Inlp To Be Published.
Page generated: Wed Jul 9 06:29:42 2025

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